3D prestack depth migration is an important and commonly used way to obtain the images of complex structures in seismic data processing. In this paper, 3D prestack depth migration with hybrid four-way splitting scheme is investigated. Wavefield extrapolation is based on the 3D acoustic one-way. The hybrid four-way splitting algorithm based on factorization is derived. Numerical calculations of 3D post-stack depth migration for an impulse and 3D prestack depth migration for SEC/EAEG benchmark model are implemented. The result of 3D post-stack depth migration show that the numerical anisotropic errors can be reduced effectively and the errors are small when the lateral velocity variations is small. Moreover, the 3D prestack depth migration for SEC/EAEG model both with two-way and four-way hybrid splitting scheme can yield its good images. The Message Passing Interface (MPI) programme is adopted on PC cluster as the large scale computation of 3D prestack depth migration. The parallel efficiency is high because of high parallel feature of 3D prestack depth migration. The methods presented in this paper can be applied in field data processing.