The invention relates to the technical field of power grid dispatching and management, in particular to a seamless switching control method for an energy storage system. A reconfigurable PI (proportional integral) controller is adopted to replace an existing common PI controller, and the control strategy that PQ and VF modes are operated synchronously is combined, namely, when the energy storage system is operated, a PQ control module and a VF control module are all operated, but only the control result of one control module under the operation module is inputted to the control in the next link, the output result of the other control module is not inputted to the next link and is shielded, and no control effect is generated. Therefore, the seamless switching of grid separation and connection of the energy storage system is realized, the seamless switching is realized under the circumstance that the power supply for users is not interrupted, and the quality of electric energy is improved.