Wave-CAIPI is a novel 3D imaging method with multiple-channel coils and corkscrew trajectories in k-space to speed up magnetic resonance imaging acquisition. However, the 3D data acquisitions of Wave-CAIPI are usually time consuming. In order to accelerate the reconstruction procedure, we realized a Wave-CAIPI reconstruction method using a modified GPU-based conjugate gradient algorithm to reduce time cost of the image reconstructions. The experiments of phantom and in vivo human brain show that the proposed GPU-based Wave- CAIPI reconstruction can achieve similar imaging results with less time cost, comparing to the conventional CPU-based Wave-CAIPI reconstruction.