The agreement, made during the first formal talks since 1999, will allow weekend charter flights starting in July. Critics say that Taiwan has made too many concessions too quickly.
Journalist Fareed Zakaria writes of the rise of new global powers.
Taking office Tuesday, Mr. Ma promised closer economic ties and more talks with Beijing.
Taiwan's vice-president elect meets with mainland China about a cross-straits economic stimulus plan.
Ma Ying-jeou, a former mayor of Taipei and Harvard Law School graduate, may face resistance to his conciliatory approach.
The resurgence of pro-China opposition party, Kuomintang, which took a majority in Saturday's legislative elections, boosts its chances for the presidential vote in March.