More than 100 Buddhists gathered at the Guangji temple in Beijing, which was originally built in the Jin Dynasty (1115-1234), to mourn the victims and pray for their relatives.
Master Xuecheng, head of the Buddhist Association of China, said people from both sides of the Taiwan Straits share the same religious culture and traditions.
"We always appreciate the help from Taiwan when the mainland is hit by major disasters, such as the Wenchuan earthquake in Sichuan province in 2008," he said.
"I hope people from both sides can again support each other and weather the disaster." He said the association has collected more than 500,000 yuan ($77,000) in donations.
Nelson Chuang, deputy director of Beijing's Taiwan Company Association, attended the prayers and said he comes from the disaster area.
"I am lucky that nobody from my family was hurt. I am praying for other people in my hometown," he said. "I am very grateful that people on the mainland also care about Taiwan. We are a family even though there is a Strait between us."
Prayer meetings were also held at Beijing's Baiyun temple, a well-known Taoist temple, and several Mazu temples in Fujian province, which shares most traditions with Taiwan.
Mainland netizens also voiced their sympathy and prayers on the Internet.
Toutiao Xinwen, a micro-blog account with more than 40 million followers, posted "Pray for Taiwan" and a picture of candlelight tributes from last Saturday when the quake struck southern Taiwan. The post received more than 4,000 "likes" in an hour.
The death toll from the quake stood at 98 as of Friday night, with about 26 people still missing.
The collapse of the 16-story Wei Guan Building in Tainan, the building most seriously affected by the quake, accounted for 96 of the deaths, according to authorities in Taiwan.
Rescuers said the chances of finding survivors from the wrecked building are now slim, but the search will continue.
The quake, which the China Earthquake Administration said had a magnitude of 6.7, hit the city of Kaohsiung at 3:57 am last Saturday, just two days before Spring Festival. Local monitoring authorities put the scale of the quake at 6.4.
Leading political figures, including Taiwan leader Ma Ying-jeou and the island's leader-elect Tsai Ing-wen visited Tainan to attend mourning ceremonies on Friday.
