Huang Bowen started his football career with Beijing Guoan when he was promoted to the club's first team in the 2004 season.

It wasn't until the 2007 season that Huang started to establish himself as an integral member of the Beijing squad, helping them finish as runners-up in the league.

On 13 August 2017, Huang suffered a lumbar fracture during a league match against Henan Jianye when he was knocked off balance by Ricardo Vaz Tê, which ruled him out for the rest of the season.

On 29 March 2016, Huang opened the scoring in a 2–0 home win against Qatar in the last game of the second round of the 2018 FIFA World Cup qualification (AFC).

The goal was widely regarded as an iconic moment in Huang's career as well as Chinese football history, as the win saw China reach the final round of World Cup qualifying stages for the first time since 2001.