To minimise the damage to relations caused by the Tibetan spiritual leader's visit, Taiwan canceled his second prayer meeting for typhoon victims, scheduled to be held Thursday.
The Dalai Lama arrived Sunday night for a four-day visit.
Beijing accuses the Dalai Lama of promoting independence for Tibet, while he maintains he only wants greater autonomy for the region.
China accused the DPP of plotting the visit to sabotage Taipei-Beijing ties, which have been improving rapidly since President Ma Ying-jeou took office last year.
China still regards Taiwan a breakaway province awaiting reunification.
The launch of regular flights marks a milestone in Taiwan-China ties. Previously Taiwanese going to China had to change flights, usually at Hong Kong, while Chinese citizens were not allowed to visit Taiwan.
As cross-strait tension began to thaw, Taiwan and China launched holiday charter flights in 2003, which were expanded to weekend charter flights in July 2008 and upgraded to daily charter flights in December.