The fan protest came as the international hub is rocked once more by huge anti-government protests with record marches over the weekend and demonstrators seizing major highways on Wednesday morning.
The latest protests have been sparked by a proposal to allow criminals to be rendered to China for the first time.
Many are fearful the proposed law will drag people into the mainland's opaque courts in politically motivated trials and hammer Hong Kong's reputation as an international business hub.
Footage posted on social media from Hong Kong's 0-2 defeat by Taiwan on Tuesday night showed fans booing loudly as China's "March of the Volunteers" anthem was played.
Fans have booed the national anthem for years but it has become much more commonplace ever since huge pro-democracy protests in 2014 failed to win any concessions from Beijing.
China bristles at any disrespect of its anthem and has fine-tuned legislation on the proper way and place to sing the anthem, tightening rules that already bar people from performing it at parties, weddings and funerals.
Earlier this year Hong Kong unveiled a proposed law that would punish anyone who disrespects the Chinese national anthem with up to three years in jail.
The legislation, which specifically mentions fan behaviour at football matches as part of its justification, is still making its way through the city's parliament.
A draft bill showed that the city planned to copy the mainland by bringing in a maximum three year prison sentence for "serious" cases of disrespect towards the national anthem.
The draft outlaws playing the anthem "in a distorted or disrespectful way, with intent to insult". It also forbids altering the anthem's lyrics and its score. As well as possible jail time, offenders will also face fines of up to HK$50,000 (around $6,000).
Critics of the bill have described it as yet another move by the city's pro-Beijing authorities to stamp out dissent and criticism of China in a city where free speech is supposed to be protected.