Reliable runoff prediction plays a significant role in reservoir scheduling, water resources management, and efficient utilization of water resources. To effectively enhance the prediction accuracy of monthly runoff series, a hybrid prediction model (TVF-EMD-SSA-ELM) combining time varying filtering (TVF) based empirical mode decomposition (EMD), salp swarm algorithm (SSA) and extreme learning machine (ELM) is proposed. Firstly, the monthly runoff series is decomposed into several sub-series using TVF-EMD. Secondly, SSA is used to optimize the input weights and hidden layer biases of the selected ELM model. Finally, the prediction results are generated by summing and reconstructing each sub-series based on the SSA optimized ELM model. This hybrid model is applied to the monthly runoff prediction of Manwan hydropower, Hongjiadu hydropower, and Yingluoxia hydrological station, and compared with back propagation (BP), ELM, SSA-ELM, PSO-ELM, GSA-ELM, TVF-EMD-ELM, EMD-SSA-ELM, extreme-point symmetric mode decomposition (ESMD)-SSA-ELM, wavelet decomposition (WD)-SSA-ELM and complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN)-SSA-ELM models. The prediction performance of various models is reflected by four evaluation indicators (R, NSEC, NRMSE, MAPE). Results reveal that the prediction effect of the ELM model is better than that of BP, the optimization accuracy of SSA is better than those of particle swarm optimization (PSO) and gravitational search algorithm (GSA), and the prediction accuracy of the hybrid TVF-EMD and SSA is better than that of only TVF-EMD or SSA. TVF-EMD-SSA-ELM model has the highest prediction accuracy. When compared with the single ELM model, it’s NRMSE and MAPE at Manwan hydropower decrease by 84.4% and 72.38%, those of Hongjiadu hydropower decrease by 85.21% and 78.38%, and those of Yingluoxi hydrological station decrease by 68.42% and 39.51%, respectively. R and NSEC of the three sites are close to 1. Therefore, the proposed model provides a new method for the prediction of monthly runoff, and the results can provide a reference for the prediction of monthly runoff in the study area.