Excessive deflection and its long-term sustainable development has become a common disease of large span pre-stressed concrete continuous box girder bridge, but the causes of it is difficult to reach consensus. A three-spans continuous pre-stressed concrete box girder bridge is studied in this paper. The web inclined cracks near L/4 of the continuous girder bridge is simulated by FEM (finite element method), in order to explore the influences of web inclined cracks near L/4 on the overall deflection of the bridge and the effect differences of the crack width, length and numbers. The results show that when the web inclined cracks reach a certain level, it will cause a long-term sustainable development of the deflection of the bridge. Therefore, web inclined crack is the main factor that causes the sustainable development of long-term deflection of large span pre-stressed concrete continuous box girder bridges.