Civil aircraft fuel tank system lightning prevention is an important research area of fuel tank safety. According to FAA amendment No.25-146 and AC25.954-1, this paper introduces the fuel tank system lightning prevention analysis method. Based on the analysis method of ignition source protection, the ignition source caused by lightning can be analyzed separately through fault-tolerant design and non-fault-tolerant design after clarifying the lightning zoning of aircraft. For fault-tolerant designs, compliance can be demonstrated only by proving that the protection design features are effective and reliable, without further analysis of failure probability. For non-fault-tolerant designs, it can evaluate through by qualitative and quantitative analysis methods. In the qualitative analysis, it is necessary to evaluate that the probability of non-fault-tolerant feature failure and the ignition source is remote. In the quantitative analysis, it needs to combine the probability of the fuel tank flammability, the probability of critical lightning strikes, and the failure probability of protective features to ensure that the probability of fuel vapor ignition caused by lightning is extremely improbable. At the same time, the effectiveness of the protection design features is verified according to the current amplitude and waveform defined by the lightning environment.