Taiwan claims the island - which it calls Taiping but is also known as Itu Aba - in the Spratly archipelago, a chain also claimed by China and other neighbours.
Mr Ma, who is seen to be friendly towards China, has less than four months left in his presidency.
Incoming president Tsai Ing-wen will not send a representative on the trip.
China claims most of the South China Sea, including the Spratly Islands. It also sees Taiwan as a breakaway province that will eventually be reunited with the mainland.
Some or all of the Spratly Islands and their surrounding waters are also claimed by Taiwan, the Philippines, Vietnam, Malaysia and Brunei.
"The Taiping Island is an inherent part of the Republic of China's territory," said Charles Chen, spokesman of the presidential office, using the official name for Taiwan.
He said the purpose of the trip was to visit Taiwanese personnel based there, ahead of the Lunar New Year holiday.
Mr Ma will address reporters at a press conference after his trip, he added.
The spokesman for China's Taiwan Affairs Office which handles cross-straits relations, said in response that China had an "undisputable authority" over islands in the South China Sea.
"Protecting the rights of the country and keeping its territory whole, protecting the rights of the Chinese, are the shared responsibilities and duties of China and Taiwan," said Ma Xiaoguang.
Taiwan has been building up a presence on Itu Aba/Taiping, constructing a lighthouse and upgrading a port. The largest natural island in the Spratly chain, it also has its own airstrip and a hospital.
It is now the fourth biggest island overall in chain, after China's land reclamation activities on Mischief Reef, Fiery Cross Reef and Subi Reef, said Taiwan's coastguard last year.
About 180 people live on the island which saw its last presidential visit in 2008, most of them coastguard personnel.
Outgoing Taiwanese President Ma Ying-jeou is to visit a disputed island in the South China Sea on Thursday.