Pile raft foundation is a method to deal with the insufficient bearing capacity of soft soil foundation, which is widely used in civil buildings, mainly to solve the problem of insufficient vertical bearing capacity; For the nuclear island building in nuclear power plant, the research and application of pile foundation are very lack. Because the nuclear island is subjected to the earthquake with a return period of 10,000 years, the problem of horizontal bearing capacity has become particularly prominent, which cannot be covered by the existing codes in some aspects, especially the problem of uneven shear distribution of pile groups. In this paper, taking the AP1000 Nuclear Island plant as an example, the uneven distribution of shear force is studied. The pile raft model and AP1000 model with foundation piles are calculated and analyzed by using the finite element program ANSYS. The influence of the connection form of pile and raft, the stiffness of raft, superstructure and torsion on the uneven distribution of shear force of pile groups is studied, which provides a basis for engineering design.