China considers Taiwan to be part of its territory and has refused to rule out using force to bring the self-ruled island under its control.
The incident happened Wednesday during a men's doubles match in the BWF World Tour Finals in Hangzhou city in the eastern province of Zhejiang.
Two-time Olympic gold medallists Lee and Wang were playing another Taiwanese pair when a spectator shouted: "Lin-Yang, Taiwan belongs to China, did you know that?"
Other fans began cheering, clapping and chanting "China, Taiwan" as Lee and Wang stood on the court smiling and laughing, a video posted on the social media platform X showed.
Taiwan's Sports Administration told AFP it had ordered the island's badminton association to "file a formal protest" over the spectators' "provocative actions".
"Such behaviour will only cast a shadow on future sports exchanges across the Taiwan Strait," the Sports Administration said in a statement Friday.
The administration called on the international governing body BWF and the Hangzhou organisers "to take necessary actions to prevent such political interference" and avoid affecting the performance of players.
Taiwan's badminton association told AFP on Friday it had not yet received a response from the BWF.
The BWF declined to comment when contacted by AFP.
After winning the match, Lee posted on Facebook: "We agreed to enjoy this tournament and smile more on the court. Although the first match was a 'civil war', it felt great to fight alongside you all."
While Taiwan regards itself as a sovereign nation, China has sought to erase it from the international stage.
Taiwan competes under the name Chinese Taipei in international sports events due to pressure from China, which baulks at any attempt to give the island legitimacy.
