In 2000, as a senior Chong was selected for the South Korea national baseball team for the 2000 Summer Olympics held in Sydney, Australia. As the only amateur player on the 24-man roster, Chong started two critical games against Team USA, facing Roy Oswalt as a starter in both of the games. In the first game against the United States in the round-robin, he pitched seven scoreless innings with five strikeouts, allowing six hits. In the semifinal game against the United States, he gave up only two runs and five hits in 6.1 innings with six strikeouts. Due to his impressive performance, Team South Korea eventually won their first Olympic medal.
In 2002, Chong had a better season, pitching 42 innings in 24 games with a 3.21 ERA and 30 strikeouts. In November, he was selected for the South Korean national team and led his team to the silver medal at the 2002 Intercontinental Cup. In the round-robin tournament, Chong racked up 11 strikeouts against Panama, allowing 2 runs and 6 hits in 5.2 innings pitched, and pitched a 5-1 complete game victory over Dominican Republic. Chong started for South Korea in the gold medal game, and allowed 2 runs over 6 innings in a 1-2 loss to Cuba. He tied José Ibar of Cuba for the Cup lead in strikeouts.
In the 2003 season, he pitched 51 innings in 37 games, going 4-3 with a 2.29 ERA, 2 saves and 8 holds, allowing 33 hits, 4 home runs and 13 earned runs.
In 2004, Chong appeared in 52 games with 69.1 innings pitched and posted a record of 2-3 with a 2.34 ERA, 2 saves and a career-best 16 holds, allowing 62 hits and 2 home runs.
In 2005, Chong got an injury at his arm and missed the first half of the season, undergoing arthroscopic surgery. He came back from injury in the second half of the season and posted a remarkable ERA of 0.37, racking up 3 saves and 6 holds and allowing only 1 earned run in 24.1 innings pitched.
Chong had his career-best season in 2007, when Cabrera left via free agency to the Lotte Giants and Chong became the full-time closer for the Wyverns. Chong posted career-highs in saves (27) and strikeouts (65) with a 0.92 ERA, and allowed only 50 hits and 3 home runs in 78.1 innings pitched. He became the first pitcher to have a sub-1.00 ERA in 70+ innings pitched since 1995, when South Korean pitching legend Sun Dong-Yeol posted a 0.49 ERA in 109.1 innings pitched.
In 2010, Chong was sidelined in the early part of the season due to a chronic knee problem. He came back to the bullpen in May but was demoted from his role as Wyverns closer, losing the job to Lee Seung-Ho. Chong completed a strong season as a flexible set-up man and an occasional closer as well, posting a 1.40 ERA with 8 holds and 4 saves in 49 games.