Direct air, shipping, and postal links were halted after Taiwan split from China following the 1949 Civil War. Flights between China and Taiwan later resumed, but only flew on weekends and during major holidays and festivals.
Beijing considers the self-governed island to be part of its territory and has not ruled out military action to prevent the province from breaking permanently from the mainland. Currently, 23 states maintain formal diplomatic relations with Taiwan.
The historic agreement on resuming direct links was signed in November.
On Monday, some 90 ships will be able to conduct direct trips from 63 Chinese ports and 11 Taiwanese harbors across the Taiwan Strait. Experts believe the move will save up to $25 million per year.
"Given the global financial crisis, cross-Strait direct journeys have started at exactly the right time," the Xinhua news agency cited Zhang Lizhong, a deputy director of China's State Council for Taiwanese Affairs, as saying.
Direct links, he added, would also "help the mainland and Taiwan jointly overcome the current (economic) difficulties."
There are now to be 108 passenger flights every week, and 60 return cargo flights per month, Xinhua said.
The first flight left from the southern Chinese city of Shenzhen for Taiwan at 7:20 a.m. (23:20 GMT Sunday).
