Due to the absence and hysteresis of the internal control system of social insurance agencies in some areas,the security of social insurance fund management is left largely examined by public. Meanwhile,migrant workers need a new social insurance system different from the established one. Thus it is necessary to take an in-depth exploration on the internal regime of social insurance. Based on the introduction of the internal control theory,this paper analyzed the general condition and plight of the internal control system of social insurance agencies and the special requirements of migrant workers’social insurance work. Finally it put forward some proposals to improve the internal control system of social insurance agencies：strengthen the awareness of internal controls,further clarify the responsibilities of the social insurance agencies,use electronic means to control risk，and establish information communication mechanism and risk prediction mechanism and so on.