The value of the deal for Youbibi, which was founded four years ago in Shenzhen and employs 20 people, was not disclosed. It specialises in domestic travel, hotels and flights for Chinese nationals.
Skyscanner, which has its headquarters in Edinburgh, has had its own office in Beijing since 2012.
The company said it will start to integrate the Youbibi service under the Skyscanner banner in the coming months although it would retain engineering teams in both Chinese cities.
Gareth Williams, Skyscanner chief executive, said the company has seen the numbers of visitors to its sites and apps grow tenfold across China since setting up a dedicated team there.
However he feels the opportunities for growth remain compelling and said: "This acquisition brings the best of both worlds with Skyscanner's international coverage and Youbibi's domestic travel search and intimate knowledge of the Chinese traveller.
"The acquisition takes us from being a strong international travel specialist in China to a truly global travel service provider for Chinese nationals, domestically and internationally."
Around 20 per cent of all Skyscanner's visitors come from the Asia Pacific region.
In February this year monthly unique users were said to be around 25 million.