With the continuous progress in integrated circuit technology, single-event effect (SEE) has become a key factor affecting the reliability of aerospace integrated circuits. Simulating fault injection using the computer simulation technique effectively reflects the SEE in aerospace integrated circuits. Due to various masking effects, only a small number of faults will result in errors; the traditional method of injecting one fault in one workload execution is inefficient. The method of injecting multiple faults in one workload execution will make it impossible to judge which fault results in errors because the propagation characteristic of SEE and faults may affect each other. This paper proposes an improved multi-point fault injection method to improve simulation efficiency and solve the problems of the general multi-point fault injection method. If one workload execution does not result in errors, multiple faults can be verified by one workload execution. If one workload execution results in errors, a specific grouping method can be used to determine which faults result in errors. The experimental results show that the proposed method achieves a good acceleration effect and significantly improves the simulation efficiency.