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We design two novel waveguides in membrane-stack photonic crystals and obtain their dispersion characteristics by the three-dimensional (3D) plane wave-expansion method.The 3D photon control phenomena are demonstrated,in which light is incident on the crystal and is bent both horizontally and vertically.Then light is split into two and is finally emitted from the other side of the crystal.A 3D splitter is realized.We also present a nanocavity to trap photons.With waveguides of different directions and nanocavities,the arbitrary 3D photon manipulation has been demonstrated.