This paper derived the mathematical expressions of short-circuit current (SCC) of permanent magnetic synchronous generator, which are applicable to different types of faults under decoupled sequence control (DSC). Based on the calculation method, the effect of PI controller saturation on SCC was also analyzed. Finally, the formula calculation results were compared with that of PSCAD simulation and manufacturer-based black-box model, which verified the effectiveness and accuracy of the proposed method. The influence of PI controller parameters on transient SCC was also illustrated in this paper.