The invention discloses a control system for a methanol reforming fuel cell power generation system under a variable load working condition, and the system comprises a fuel supply module, a methanol reforming module, a fuel cell module, an energy storage module, and a control module. Staged control is carried out according to the characteristics of the methanol reforming fuel cell system, regionalization processing is carried out on the power required by the user and the residual capacity of the energy storage module, and difference and delay adjustment is carried out on the output power of the methanol reforming fuel cell system according to the power required by the user and the residual capacity of the energy storage module. According to the invention, the methanol reforming fuel cell system can be quickly recovered and kept in a relatively good state for a long time, the defect of slow response of the methanol reforming fuel cell system is overcome, the impact of variable user demand power on the methanol reforming fuel cell system is avoided, and the requirements of users on global variable user demand power and discontinuous power utilization are met; and efficient and stable operation of the whole power generation system can be ensured.