In a letter to its customers this week, IDS accused the trade body of bowing to "ITV demands for a trebling of its voting power and an exclusive right of veto".
The Thinkbox chief executive, Tess Alps, confirmed the trade body would benefit from a "substantially bigger budget", but declined to reveal the exact size of its new funding. Its current budget stands at around £3 million.
The new budget will be available to spend from September this year.
IDS, which sells airtime on behalf of Living TV, Bravo and UKTV Gold, was part of an original structure based on one company, one vote, regardless of financial contribution. The new structure, which is still based on share of TV ad revenue, hands the bigger contributors a greater share of voice on some issues.
Alps said: "The old system wasn't practical or realistic. We operate on a one man, one vote system on the majority of issues, but not on major financial issues. It's very sad that IDS has chosen to resign."
James Wildman, IDS's executive sales director, said: "We will do everything we can to complement Thinkbox."