Bidirectional DC/DC converter has the characteristics of dual quadrant of the energy transformation and hybrid of multi-model. In order to solve the shortcomings of ignoring its high frequency dynamic characteristics、the precision model is too large, and the characteristic of hybrid is not considered in the existing models,such as average model and accurate model. First of all, the continuous state differential equations of the working modes are established, then, a hybrid automata model is established which can fully describe the working modes based on the theory of hybrid automata, finally, the control algorithm is designed based on the hybrid automata model. MATLAB/stateflow is used to simulate the control algorithm, the results show that the hybrid automata model of bi-directional DC/DC converter has the advantages of small amount of calculation, high precision, reflecting the high frequency dynamic characteristic of the system, in particular, it fully describes the various working modes of the system, the CCM mode and DCM mode are considered, the control algorithm based on hybrid automata model is simple and effective, which is in line with the practical application.