Competing under the name Chinese Taipei, Taiwanese athletes brought home seven medals -- two gold and five bronze -- the second-best result for the island in an Olympic Games.
Lin clinched gold in the women's boxing final match on Sunday, an emotional win that came as she and Algerian boxer Imane Khelif have been embroiled in a major row over their gender eligibility.
"I would like to thank Lin Yu-ting on behalf of the people," leader Lai Ching-te told the party, hosted at the presidential office.
"But this time you won the respect and admiration of the people not just because how you performed in the boxing ring. It's the high standards and grace you showed outside the boxing ring," he said.
"You are not afraid of any attack. It's admirable that you still uphold the sportsman's spirit... everyone is proud of you."
Lin said in a speech at the party that she was "honoured" and thanked "the country and the people" for their support.
Both the Taiwanese government and the public have thrown their support behind Lin -- who has been dubbed "Taiwan's daughter" by the local media.
Hundreds of fans thronged the streets in downtown Taipei as Lin and other Olympic medallists rode in open-top jeeps in a "hero's parade".
Lin and Khelif have been the central figures in a furore that has drawn fire from the likes of Donald Trump and author J. K. Rowling.
Both were disqualified by the International Boxing Association (IBA) from its world championships in 2023, but were cleared by the International Olympic Committee (IOC) to compete in the Paris Games.
IBA's Russian president and Kremlin-linked oligarch, Umar Kremlev, has claimed that the two women had undergone "genetic testing that shows that these are men".
The IOC has leapt to the defence of both boxers, with president Thomas Bach saying they were born and raised as women, and have passports saying that. Neither is known to identify as transgender.
