In order to improve fault tolerance of three-phase four-switch shunt active power filter and increase the reliability of the filter, and for the troubleshooting of SAPF, this paper presents a fast response fault type and fault location by hybrid system dynamic model and identifying sources of error through its evolution of the residual of system output current. Fault-tolerant switching strategy is utilized to remove the corresponding fault arm, so SAPF under the circumstance of fault-tolerant model continues working. At the same time, this paper obtains the source current tracking compensation strategy, which is more suitable for fault-tolerant switching SAPF, through the study of SAPF compensation algorithm. Furthermore, feedforward control is added to eliminate influence of split capacitors unbalanced midpoint electrical potential of DC side under fault-tolerant state, the effect of compensation is more significant. Experiments and simulations verify the effectiveness of the method. This work is supported by National Natural Science Foundation of China (No. 51307076).