Using large structure analysis software, the stress and displacement are calculated for Shuangji River rectangle aqueduct structure during construction and operation periods. The 19 different load combination cases are considered. The variation rule of mechanics behavior is obtained for concrete material during different load combination period. The simulation results show that the conventional method simulating prestress can lead to stress concentration in the point the force is acted on. It is a relatively good simulation method to add a steel plate to the area where the prestressed strands are acted on. In this way, the local stress concentration can be reduced. When use pseudo-static method for calculation of the seismic load, the load case considering the seismic load is a control load case. The Shuangji River aqueduct can meet the requirement of intensity and rigidity during construction and operation periods.