This paper proposes a problem of passenger flow organization in subway stations under uncertain demand. The existing concepts of station service capacity are extended and further classified into three in different demand scenarios. Mathematical models are put forward to measure the three capacities and a unified simulation-based algorithm is developed to solve them. To increase computing speed, data envelopment analysis (DEA) and genetic algorithms (GA) are embedded in this algorithm. A case study will demonstrate the performance of the proposed algorithm and give a detailed procedure of passenger flow control based on station service capacity in various demand scenarios.