He was speaking at the Conservative Party conference in Manchester on Sunday.
A key part of the framework is a new system for moving goods from Great Britain to Northern Ireland.
Mr Heaton-Harris said he had visited the port at Birkenhead to see the new arrangement operation.
He also revealed he is considering a new ferry route between Liverpool and Larne.
Mr Heaton-Harris previously said the new system would mean "the substantial majority" of trade from Great Britain to Northern Ireland will be "treated as UK internal trade".
The most visible change will be ʼNot for EUʼ labelling appearing on some food products in Northern Ireland shops.
That labelling change is due to be rolled out across the rest of the UK next year.
The framework modifies the Northern Ireland Protocol, the 2019 deal which kept Northern Ireland inside the EUʼs single market for goods.
That arrangement keeps the Irish land border open, but has meant products arriving into Northern Ireland from the rest of the UK are subject to checks and controls.
On Sunday, a new trusted trader scheme came into effect with a system of "green and red lanes" at Northern Irelandʼs ports.
The first lorries to operate under the green and red lane system arrived in Belfast Harbour on Sunday morning.
There were 23 lorries and 31 trailers on board one of the Stena Superfast VIII ferry crossings from Cairnryan in Scotland.
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The green lane/red lane system is supposed to reduce bureaucracy for Great Britain goods which have Northern Ireland as their final destination.
Goods which are coming from Great Britain to be sold to consumers in Northern Ireland will use the green lane meaning minimal paperwork and few routine checks.
Companies will have to be signed up to a new trusted trader scheme to use the green lane.
There were some trusted trader processes under the protocol but Mr Heaton-Harris said the new scheme was open to a wider range of businesses.
The biggest change is in the treatment of food products.
Under the Northern Ireland Protocol, food products being sold in Northern Ireland had to be produced to EU standards.
That meant products coming from Great Britain faced costly bureaucracy to prove their products met the EU rules.
ʼGrace periodsʼ meant these requirements were never fully imposed on supermarkets after they warned it would make their Northern Ireland businesses unworkable.
Under the Windsor Framework, UK public health and safety standards, rather than EU standards, will apply for all retail food and drink.
That means a wider range of Great Britain trusted traders who are sending food for sale in Northern Ireland will face much reduced bureaucracy.
The flipside of this is the introduction of the ʼNot for EUʼ labels on Great Britain food products, to give a level of assurance to the EU that products will not wrongly be sold in its single market.
Shoppers from the Republic of Ireland can still take goods home from Northern Ireland but cannot resell them.
Addressing his partyʼs conference, Mr Heaton-Harris said the framework was a marked improvement on the Northern Ireland Protocol.
He added Northern Irelandʼs economic prospects were now "unbelievably promising".
The secretary of state has been leading talks with the Democratic Unionist Party (DUP) aimed at addressing the partyʼs concerns over the Windsor Framework.
Northern Ireland has been without a functioning power-sharing government since February 2022, when the DUP withdrew from the executive due to its protest against the protocol.
Lack of executive
In a direct message to the DUP leadership, he said: "I say to my friends in the unionist community we will continue working to answer your remaining concerns.
"Progress has been made and we are working in a constructive spirit and it is clear the vast majority of people and their political leaders want to get this done."
Mr Heaton-Harris said Northern Ireland had been without a functioning government for 605 days at a time of great economic and health challenges.
He said up to 22 percent of the population were on a waiting list for treatment.
ʼOngoing bureaucracyʼ
James Duke, of Manfreight, one of NIʼs major hauliers, told the BBC they were not anticipating any major problems with the new systems but that one potential issue could be lack of preparedness among some GB suppliers.
But he said it would not be "a repeat of 2021" when the protocol was introduced adding that government agencies are being "very pragmatic and collaborative".
However, some businesses will face ongoing bureaucracy, particularly food wholesalers who distribute goods across NI and the Republic of Ireland.
Goods which will potentially be sold in the Republic of Ireland will not qualify for green lane processes and will instead have to use the red lane.
Andrew Lynas, who runs Lynas Foodservice in Coleraine, told the BBC that about 75% of his goods coming from Great Britain will have to use the red lane.
He gave the example of a dessert being supplied from a company in Wales.
"We may sell 100 cases of that a month, 98 of stay in NI and two could go to the Republic and yet all 100 of those have to get all the checks for the red lane.
"So itʼs difficult to get the supplier to understand and to want to, maybe, supply us."
But he said the big advantage of the framework is that it brings certainty after years of Brexit uncertainty.
Meanwhile, Nichola Mallon, from Logistics UK, said although not perfect the system was something that businesses could work with.
"What businesses are very focused on is making this work, finding practical solutions with the government to ensure the smooth flow of trade from GB to NI while also meeting the EU requirements around protection of the single market," she said.