After the 2002 season, Lee was selected for the South Korea national baseball team for the first time and competed in the 2002 Intercontinental Cup held in Cuba.

In the gold medal game, Lee hit a solo home run off Cuba's starter José Ibar in the bottom of the 4th inning to break a scoreless tie.

His stats dipped slightly in 2003, but broke out again in the 2004 season when he batted a career-high .308 with 23 home runs and 74 RBIs, playing in all 126 regular-season games as a shortstop.

In the 2009 KBO season, Lee had another solid performance, batting .284 with 25 home runs (7th in the league), 124 hits and a career-high 79 RBIs in 126 regular-season games as a third baseman.

He hit his first NPB home run on April 9, 2010, against Nippon Ham at Fukuoka Dome in the seventh inning off Hirotoshi Masui.