Speaking at the FT Digital Media conference, Thompson said that "commercial considerations will never influence" journalism decisions despite the changes to the company and industry.
He said: "Journalists, designers, computer scientists, marketers and other specialists are co-located and working incredibly closely together on projects.
"This does not mean diluting the independence of the news room when it comes to editorial decision making. We will only succeed if the news room and business side work very closely together."
Under the company’s new head of advertising Meredith Kopit Levien, the New York Times is developing new digital ad units including "paid posts" and new native advertising units as it takes a "more competitive and aggressive stance in the market".
Next week the New York Times will launch an app called NYT Now that will cost eight dollars for four weeks and be the half the cost of the current cheapest digital subscription product.
Thompson describes the app as an "express version" of Times journalism that has been optimised for the smartphone using the top stories from the website.
It comes from Thompson’s ambition to have a "ten-minute Times" and executive editor Jill Abramson’s desire for a version of the Times she had labelled "good to go".
The app will feature summarised version of stories based on core Times journalism, video content and "paid post" and native advertising units.
New York Times editors will also scan the rest of the web to summarise the "most interesting and diverting stories" from other news sources, while longer reads will be suggested in the evening when users have more downtime.
Thompson explained: "The idea is to give people a sense throughout the day of what they need to be fully briefed on what is going on throughout the world".
Currently 30% of the company’s traffic comes from outside the US, but only 10% of subscriptions come from outside the US.
The company hopes to increase international revenues by investing further in journalism and marketing outside of the US.