Taking the heterogeneity interlocking DC-DC converter as the object of study, firstly, this paper conducts the magnetic integration research on the main inductance of the converter, and proposes the design criterion of the heterogeneity magnetic coupling inductance through the analysis of normalized equivalent inductance. The research conducts the model building of the Buck mode of the converter with the small-signal, and deduces the transfer function from the state variables to control variables. Secondly, based on both the open-loop features of three-phase magnetic coupling converter and the deficiency of average current control, the control strategy of the improved average current for the bucking current loop is proposed. Finally, through the simulation and experiment, it proves that the proposed new type control strategy can optimize the stable state and transient behavior of the system compared with the traditional control mode. Meanwhile, the design of the magnetic coupling inductance also improves the phase current ripple, as well as enhances the response speed of the transient current of the converter. This work is supported by National Natural Science Foundation of China (No. 51274118).