The traditional decomposed ensemble prediction model decomposes the entire rainfall sequence into several sub-sequences, dividing them into training and testing periods for modeling. During sample construction, future information is erroneously mixed into the training data, making it challenging to apply in practical rainfall forecasting. This paper proposes a novel stepwise decomposed ensemble coupling model, realized through variational mode decomposition (VMD) and bidirectional long short-term memory neural network (BiLSTM) models. Model parameters are optimized using an improved particle swarm optimization (IPSO). The performance of the model was evaluated using rainfall data from the Southern Four Lakes basin. The results indicate that: (1) Compared to the PSO algorithm, the IPSO algorithm-coupled model shows a minimum decrease of 2.70% in MAE and at least 2.62% in RMSE across the four cities in the Southern Four Lakes basin; the IPSO algorithm results in a minimum decrease of 25.58% in MAE and at least 28.19% in RMSE for the VMD-BiLSTM model. (2) When compared to IPSO-BiLSTM, the VMD-IPSO-BiLSTM based on the stepwise decomposition technique exhibits a minimum decrease of 26.54% in MAE and at least 34.16% in RMSE. (3) The NSE for the testing period of the VMD-IPSO-BiLSTM model in each city surpasses 0.88, indicating higher prediction accuracy and providing new insights for optimizing rainfall forecasting.