"I seek a second term because I believe that Taiwan will be better and better if I continue to be the president," Ma said as he registered for the ruling Kuomintang party's primary.
Taiwan's growth hit a 23-year-high of 10.82 percent last year while the island was able to interact with China "in an atmosphere of peace of prosperity," Ma said in a statement.
He is expected to be the sole candidate in the primary while the party is due to formally nominate him next month for the January 2012 presidential vote.
Ma, 60, won a landslide victory in 2008, ending the eight-year rule of the Democratic Progressive Party which saw rising tensions with China due to its pro-independence policies.
Taiwan and China split in 1949 after a civil war but Beijing still claims the self-ruled island part of its territory awaiting to be reunified, by force if necessary.