The invention provides an electric-thermal-hydrogen comprehensive energy system operation mode optimization design method, which comprises the following steps of: 1, acquiring electric-thermal-hydrogen isolated island direct current micro-grid information at the current moment, and 2, judging the redundant state of each energy storage unit; thirdly, the output in the first step and the output in the second step serve as input, the maximum value and the minimum value of the fan mode switching boundary are calculated, and the fan unit control mode at the t + 1 moment is judged; and 4, setting the operation mode and the optimal output of each unit of the system. According to the method, the operation mode design of the electric heating combined island micro-grid with renewable energy access in a strong uncertainty scene can be efficiently provided, the control mode and the corresponding switching condition of each unit in the system can be quickly and accurately judged, and the optimal output of each unit in the system is solved by optimizing the objective function; the safe and stable operation of the system in a strong uncertainty scene is guaranteed, the operation cost of the system is reduced, and the economical efficiency and the energy utilization efficiency of electric-heat combined comprehensive energy are improved.