Metro rail transit has emerged as an effective solution to traffic congestion thanks to its speed, accuracy, and riding comfort. Most of the previous studies on this critical infrastructure have primarily focused on the seismic vulnerability, while real-world scenarios often involve multiple, interacting disasters, such as rainfall and earthquake, leading to significant waterlogging and structural damage. Relevant research has indicated a strong correlation between these two natural phenomena, typically reflecting on the preceding abnormal precipitation caused by pre-earthquake geothermal changes before seismic events. Therefore, a comprehensive analysis method is needed to account for this cascading effect on surrounding soil and subway stations. Along this line, we propose an integrated analysis approach that combines soil coefficients adjustment with finite element model seismic analysis. The soil adjustment, based on infiltration theory and slope stability analysis, simplifies the multifactor correlations in layered soil. The seismic analysis, grounded in wave theory and employing viscoelastic boundary ground motion input, has been proven accurate and efficient. To illustrate the method and examine seismic responses of subway station under varying rainfall intensities, we conducted a case study on the Daikai station prototype, which is surrounded by granite residual layered soil from Guangzhou Science City. The analysis results indicate the rainfall-induced soil softening and increased pore pressure exacerbate structural stress, particularly on middle columns and upper sidewall, leading to severe damage in conjunction with bidirectional displacement around the station.