Music career Choi Siwon

Not long after Siwon's first television appearance, SM Entertainment released an announcement that he would officially debut as one of the twelve members in a boy band. This band later became officially known as Super Junior 05, the first generation of the rotational music group Super Junior. A few months before the debut of Super Junior 05, Siwon made his first official media appearance with band mate Han Geng as one of the runway models in a fashion show by Bum Suk.

Super Junior 05 officially debuted on November 6, 2005 on SBS's music program Popular Songs, performing their first single, "TWINS (Knock Out)". Their debut performance attracted over 500 fans and also garnered oversea viewers from both China and Japan. A full studio album was released a month later, which debuted at #3 on the monthly MIAK K-pop album charts.

In March 2006, SM Entertainment began to recruit new members for the next Super Junior generation. However, plans changed when the company added in a thirteenth member and the company declared a halt in forming future Super Junior generations. The group dropped the suffix "05" and became officially credited as Super Junior. The re-polished group hit big after they released their first CD single "U" the following summer, which became Super Junior's most successful single in the music charts at the time.

In late 2007, Siwon was put into Super Junior-M, the Chinese subgroup of Super Junior. Super Junior-M is the first international music group in the Chinese music industry to have members of both Chinese and Korean descent, and brought an influence in the mainland music industry to produce multi-national music groups. The subgroup specializes in singing Mandarin songs, including versions of Super Junior's Korean songs, bringing the K-pop influence over to the Chinese music industry. Super Junior-M is the first international music group in the Chinese music industry to have members of both Chinese and Korean descent. Super Junior-M debuted in China on April 8, 2008 at the 8th Annual Music Chart Awards with the release of their first single music video, "U", a Chinese remake of Super Junior's single. The subgroup released their first Chinese-language studio album, Me, on May 2, 2008 to critical success. The album debuted on Taiwan's G-music combo charts as #2 and #1 on many of China's and Thailand's music charts. Not long after Super Junior-M's debut, they became one of the most celebrated boy bands in China. The band's popularity further skyrocketed after their highly anticipated mini-album, Super Girl was released on September 2009 and managed to receive critical acclaim from numerous Chinese critics.

Choi Siwon at SM Town Live concert in Bangkok, Thailand in February 2009.

Siwon's biggest success with Super Junior was when they released their third studio album Sorry, Sorry on March 12, 2009. The album was met with acclaimed reviews. It was their first album to debut at number one on the Hanteo Charts, selling over 29,000 copies the first day. After only a month of release, the album became South Korea's best-selling album of 2009, and ultimately sold over 250,000 copies in South Korea. It became the best-selling K-pop album in Taiwan, Thailand, China, and the Philippines, in which the latter credited the album to be the first K-pop album to reach number one in music charts from the country. The album's title single "Sorry, Sorry" became an instant hit, collecting a total of ten number-one awards for ten consecutive weeks in Korea, and stayed as number one for a record-breaking 37 weeks in Taiwan's K-pop singles chart. "Sorry, Sorry" achieved national and international success, and has since been the group's best-selling single in South Korea. The group went on to release their next album Bonamana in May 2010 which managed to outsell Sorry, Sorry, selling over 300,000 copies in South Korea.

Super Junior released their fifth studio album Mr. Simple which debuted at number one on the South Korean Gaon Chart, selling 287,427 copies. The album stayed on the chart as number one for four weeks, and sold over 441,000 copies in South Korea by October 2011. However, Siwon was unable take part in some of the group's promotions for the album due to conflicting schedules with filming for the drama, Poseidon.