The overburden of the Yellow River-crossing scheme of the Beijing-Hangzhou canal is deep，and the water level of the aqueduct of the upper span scheme is more than 30 m above the ground on both sides of the river. Aiming at the multi-level scattered staggered water saving basins of high water head lock at both ends of aqueduct，two kinds of layout schemes of chamber-basin are put forward，which are wall back high fill type and wall back low fill type. We use ABAQUS finite element software to build plane finite element models，research the spatial-temporal variation characteristics of the settlement of the chamber-basin and the bending moment of the floor of the lock chamber during the construction and service periods，and discuss the action mechanism of the high fill on the lock chamber. The results show that：1）Under the condition of natural foundation，the settlement of the chamber-basin in the two layout schemes is relatively large，and the negative bending moment of the floor generated by the drag down force and side load of the high fill on the back of the wall basically counteracts the positive bending moment generated by the soil pressure，which leads to the little difference of the bending moment of the floor in the two schemes and is always controlled by the negative bending moment. 2）The foundation treatment method is one of the key technical problems to reduce the settlement of the chamber-basin and improve the stress condition of the lock chamber. 3）The method of multi-pile combination treatment of lock chamber and wall back filling and the method of drainage consolidation preloading of the filling outside foundation pit are worthy of further study.