The change is another step towards normalising travel arrangements between the two sides which have enjoyed increasingly close business ties over recent years, and follows the launch last week of their first telephone hotline.
It comes days before Taiwan goes to the polls for elections likely to put into power a political party that Beijing distrusts.
Chinese President Xi Jinping and Taiwan President Ma Ying-jeou met in Singapore at a historic summit in November, the first in 66 years.
China and Taiwan have been ruled separately since defeated Chinese Nationalist forces fled to the island in 1949 after losing a civil war to the Communists.
Beijing has never renounced the use of force to bring the island of 23 million people, which it calls a renegade province, back under its control, particularly if it were to make moves towards formal independence.
Up to now, mainland citizens have been allowed to travel to Taiwan but are not allowed to travel on from there to another destination. Airlines from both sides operate between the mainland and Taiwan.
China's Taiwan Affairs Office said in a statement on its website that passengers flying from Nanchang, Kunming and Chongqing will be allowed to transit through Taiwan's main international airport before flying on to third destinations.
Mainland passengers in transit will not be allowed to leave the airport, it said, adding that the plan would be implemented after preparatory work between the two sides was completed.
Taiwan's President Ma had expressed his appreciation of the plan, his office said in a statement, and EVA Airways, Taiwan's second-biggest airline, also welcomed it.
"It's a joint effort by governments across the strait. We're happy to see it happening," K. W. Nieh, a senior vice president at the airline, told Reuters.
"We hope more cities will be added to really implement it."
The island's independence-leaning Democratic Progressive Party is on track to trounce the China-friendly ruling Nationalists (KMT) when Taiwan votes in a new president and parliament on January 16.