The traditional symmetrical components fault analysis method may not be practically feasible in analyzing simultaneous faults， especially， in inherently unbalanced power systems because of the difficulties encountered in the assembly of sequence networks and their solution. To alleviate these problems， this paper presents a new algorithm suitable for the analysis of various complex faults in inherently unbalanced power systems on the basis of multi-port theory and optimal phase components model. By matrix transformation， the traditional phase components method is optimized to reduce the computational costs. Based on the multi-port theory， a common mathematical model suitable for computer applications is derived that can be used to analyze all kinds of simple faults and complicated faults. Simulation results verify the effectiveness of the proposed method.