Passenger flow in the metropolitan suburban rail includes urban passenger flow, suburban passenger flow, and intercity passenger flow. Regarding the operation mode when connecting to the subway, the hub transfer mode and the through operation mode are two possible choices, with the latter providing strengthened service for intercity and suburban passengers. To achieve more accurate forecasts and support better decision-making regarding the suburban rail operation mode, this study highlights that the prediction model for metropolitan suburban rail passenger flow needs to be further optimized on the basis of the “four-step model.” Passenger flow should be divided into three categories: urban areas, suburbs, and intercities. The trip generation, distribution, and mode choice steps should be performed for each of the three types of flows. After aggregation of the ODs of the above three types of flow, the traffic and transit assignment can be performed for all of them simultaneously. Furthermore, the extended four-step model widely used in advanced countries, which can feed back congestion to the whole model and dynamically balance the demand and supply, should be applied. The proposed improved model was applied to the case of the Wuxi-Jiangyin metropolitan suburban rail that will be operated with Wuxi Metro Line 1. The results verified the feasibility of the proposed model and showed that more passenger flows are expected under the through operation mode. Compared to the hub transfer mode, the daily passenger flow can grow by 16% and the peak-hour peak-section flow can grow by 7.8%. The proposed method can be applied to similar cases in other regions and better support operational decision-making.