Taiwan and China, which are 160km apart, agreed in November to the new routes that include 108 direct daily flights a week, 60 cargo flights a month and a raft of sea routes.
The new links will end the costly delays of having to go via a third country's air space or territorial waters, while also providing one of the most tangible signs of renewed ties.
China has affirmed its sovereignty over self-ruled Taiwan since 1949 and vowed to bring the island under its rule.
Tensions brought the two sides repeatedly on the brink of war over the last 60 years in what is considered potentially one of the most dangerous flashpoints in Asia.
Ma's election changed the political atmosphere and top officials from both sides met in June for the first direct talks in 10 years.
The meeting led to the launching of regular flights along with other measures to increase tourism.
Taiwan expects ocean shippers to save $1.2bn-a-year and air passengers to save at least $3bn annually while direct postal links are expected to cut current delivery time.
Annual trade between China and Taiwan is currently worth around $ 100bn a year.