In this paper, we present a new 3D structure for InP based avalanche photodiode, aiming at decreasing the excess noise factor. To the best of our knowledge, it is the first time to propose new device designs based on recently developed 3D spatial dead space model in 2014. In addition, we also propose a methodology, the 2D planar absorption distribution projection technique, for further optimizing the 3D model. According to our theoretical simulation results, by combining photonic crystal (PC) and selective area doping, the effective k values of InP and In0.52Al0.48As can be reduced to as low as ~0.19 and as ~0.13, respectively. Meanwhile, the optimal thickness of multiplication region is larger than 0.45 μm, which reduces the tunneling effect. The detailed parameter optimization process, including optics, electronics and material, is comprehensively presented. The examples in this paper also provide a fresh idea for researchers to foretell and design new photodetectors with 3D structure.