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In this paper, we present a new 3-D structure for the InP-based avalanche photodiode, aiming at decreasing the excess noise factor. To the best of our knowledge, it is the first time new device designs based on the recently developed 3-D spatial dead space model in 2014 have been proposed. In addition, we also propose a methodology, i.e., the 2-D planar absorption distribution projection technique, for further optimizing the 3-D model. According to our theoretical simulation results, by combining photonic crystal and selective area doping, the effective k values of InP and In_0.52Al_0.48As can be reduced to as low as ~0.19 and as ~0.13, respectively. Meanwhile, the optimal thickness of the 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 the 3-D structure.