Thompson spoke at today's Marketing Society's Brave Conference, where he discussed how Donald Trump's election to US president has both bolstered digital subscriptions and brought attention to bear on journalistic veracity.
"Everything we do should be worth paying for and the future of journalism is a direct relationship with a consumer who pays for quality journalism," Thompson said.
"I think advertising is a very valuable secondary stream, but the future is about a more understanding relationship based on mutual trust with the audience."
The New York Times has a total of 3.5 million subscribers, with more than two million digital subscribers, while digital revenue is continuing to grow in the last five years at about 11% a year.
"I don't know of any other news organisation that's driving that kind of revenue," Thompson said, adding that a significant portion of recent subscriber surge has been due to Trump's election to office.
"It was an unexpected result," Thompson said. "But then something else happened. Our audience had grown enormously. Crucially, it grew massively through the election, but stayed much higher than before the election started."
"On one level, our subscriptions were building on the back of this, the very opposite of what Uncle Donald claimed was happening. But on another, we were at the centre of attention and felt we were being increasingly defined by both our attackers and defenders."
Thompson talked animatedly about Trump's targeting of the media, naming and accusing specific newsbrands of reporting "fake news", when he was the one using Twitter to tell "essentially untruths directly".
It led to Thompson take an unprecedented step for a newspaper organisation, talking to his head of brand marketing and ultimately resulting in the hard-hitting "The truth is" campaign.