Abstract: This paper introduces the establishment of multi-aquifer system's mathematical model, according to conception of multiaquifer system in plain area. Based on that mathematical model, the programming flowchart for multi-aquifer system is designed, providing an available method and idea for model calculation. In accordance with the characteristics, such as multi-layer, multi-node and highly spare linear matrix equation of multi-aquifer system, the solution of conjugate gradient method and SSOR-conjugate gradient method is presented for comparison. Taking the calculation of three layers in eastern Songliao Basin as example, the forecast for water level changes caused by further groundwater recovery is conducted. Based on that larger water cones will occurrence individually in Mingshi Interval No.1 and Interval No.2 in 2005, and the depth and scope of water cone in Inter-val No.2 is larger than that in Interval No.1. The research on multi-aquifer system, therefore, is of practicability and flexibility.