Four Mirage fighter jets, firing flares, and flying above the flight escorted the flight before it landed in Taoyuan airport near the capital Taipei, where crowds welcomed the team shouting pride of Taiwan and carried signs indicating national players welcoming home.
With 11 medals thus far in Taiwan, Taiwan's performance brought jubilation on the island, with politicians and celebrities joining in to tag their social media celebrations Team Taiwan and Taiwan is Taiwan.
It also revives a debate on whether it should compete in Beijing rather than Chinese Taipei, a name used at the insistence of Taiwan, which sees the island as part of one China and has threatened to use force to bring the democratically run island under its control.
China regularly presses international organizations and companies to refer to Taiwan as part of China, saying that it has no right in any sphere to Recognition in any sphere as a separate country.
It's a dead end to seek independence in sports events with petty tricks, China's Taiwan Affairs Office said in a statement to Reuters on Tuesday.
Among those returning home on Wednesday were Lee Yang and Wang Chi-Lin, who beat Taiwan on Saturday to win the badminton men's double gold medal and became a sensation by proclaiming their Taiwan identity on social media.
This is my first time seeing a fighter jet. It is very cool, Wang, who was met by cheers, told reporters.
In a Facebook post with photos of a jet flanking a passenger plane and pilots preparing for the escort mission, Taiwan's defence minister thanked the athletes.
You show the World Indomitable Taiwan spirit, the Ministry wrote.
In China, the celebration of Taiwan identity on the island has ignited local anger, especially after TV star Dee Hsu, who has a major following in Taiwan, referred to the island's Olympians as national athletes.
Go back to Taiwan, a Social Media poster wrote on China's social media Twitter-like Weibo.