Mr Grayling told MPs: "I think Cardiff Airport's been a great success story and I pay tribute to all of those involved in it".
He was responding to a question from Newport West Labour MP Paul Flynn, who asked him to "welcome the purchase of the airport by the Welsh Assembly".
In 2013, Welsh Tories criticised Labour ministers' purchase of the airport.
Welsh Conservative leader Andrew RT Davies said at the time he was "yet to be convinced that a 1970s-style nationalisation is the answer to the airport's problems".
He later accused the Welsh Government of a "stunning failure to safeguard taxpayers' money" for paying £52m for the airport, double an initial valuation of £20m-£30m.
Ministers dismissed BBC reports based on that first estimate, by accountants KPMG, as "entirely selective and misleading".
Cardiff Airport reported a 16% rise in passenger numbers in 2016.
On Thursday, Mr Grayling said the UK was "fortunate" to have "some very good regional airports" that would be a "crucial part of our overall airport strategy in the future".
A spokesman for Welsh Government Economy and Infrastructure Secretary Ken Skates responded: "With record passenger numbers, new routes and sustained growth, the Tory Transport Secretary is right to welcome Cardiff Airport as a great success story.
"For too long Tories like Andrew RT Davies and [Welsh Secretary] Alun Cairns have sought to frustrate and talk down the good work of Cardiff Airport and the huge achievements it has made over the past few years."
A spokesman for the Welsh secretary disputed the claim, saying: "Alun Cairns is a strong supporter of Cardiff Airport and works closely with its management, as well as continuing to meet airlines interested in using it."
UK Transport Secretary Chris Grayling has paid tribute to the Welsh Government-owned Cardiff Airport.