The Chinese government has, on several occasions in the past, threatened to go to war against Taiwan if the island's authorities move to make the division permanent.
But under Ma's leadership, Beijing and Taipei have signed nine agreements on economic co-operation, including a pact that allowed for direct flights across the 160km wide Taiwan Strait.
Ma reaffirmed on Wednesday that Taiwan will not conduct unification talks with the mainland during his presidency, which would last until mid-2016 if he were re-elected.
However, he said he would continue to try to build "a solid foundation for peace and prosperity between the two sides".
Recently, Taiwan was invited to join the World Health Assembly meeting for the first time in 38 years.
It was the first time that Taiwan participated in a UN meeting since its seat was given to China in 1971, marking what Taipei regards as a major diplomatic triumph.