Muzepper was called up into China U-20's squad in 2009 where he would take part in the teams 2010 AFC U-19 Championship qualification. After China's successful qualification he would draw significant attention when he became the first Uyghur player to ever be called up to the senior team. The Chinese Head coach Gao Hongbo called him up for several training sessions in preparation for 2010 East Asian Football Championship on the basis of his youth performances, however he did not feature within the tournament. He would return to the Chinese U-20 squad and take part in the 2010 AFC U-19 Championship where he would play in three games and saw China knocked out quarter-finals. After that tournament he was immediately promoted to the Chinese U-23 squad and included in the team that played in the Football at the 2010 Asian Games where he would once more play in three games and see China knocked out in the last sixteen. On 7 September 2018, he made his debut for Chinese national team in a 1–0 away defeat against Qatar, coming on for Gao Lin in the 74th minute, which made him the first Uyghur player to appear for the Chinese national team.