However, Ma decided to enter the Eagles after graduation from college and continued to play baseball at Dankook University in Cheonan, Chungcheongnam-do.

In 2000, Ma helped his team to win the President's Flag Collegiate Baseball Championship.

As a senior in 2001, Ma led his team to win the National Amateur Baseball Championship where he was named best pitcher.

He had a mediocre rookie season, going 2-5 with 6 saves and 6 holds in 59 games and posted a 5.40 ERA in 60.0 innings pitched as a relief pitcher.

In 2003, Ma lowered his ERA to 4.06 and amassed 2 saves and 9 holds appearing in 63 games as a setup man.