Abstract: Anti-corruption in system is a fundamental way of preventing corruption from its source and the key to build corruption punishment and prevention system. Anti-corruption in system is effective with a logical motivation of overcoming the defects of human nature and an aim of avoiding the abuse of power. Its unique advantage is stability, normativity and strong operability. In order to launch the anti-corruption in university system, we must work for the institutional construction. However, there are still such obvious problems as lacking of coordination between different systems of clean government, vacancy of risk prevention and control in key fields, unsmooth running of anti-corruption warning mechanism and weak implementation of the clean system. To enhance the effectiveness of anti-corruption in university system, we should establish interests conflict management system, power operation supervision system, anti corruption early warning system and anti-corruption implementing system.