The instability toward a magnetic skyrmion crystal in centrosymmetric trilayer magnets is investigated based on a spin model with layer-dependent Dzayloshinskii-Moriya interaction. We find various types of skyrmion crystal phases with different skyrmion numbers in a low-temperature phase diagram by performing the simulated annealing. In addition to the Néel skyrmion crystal phase that is expected to emerge in the presence of the polar-type Dzayloshinskii-Moriya interaction, we obtain the skyrmion crystal phases characteristics of the layered system: the twisted surface skyrmion crystal, anti-skyrmion crystal, and high-topological-number skyrmion crystal phases. The rich magnetic phases are brought about by the synergy among the layer-dependent Dzayloshinskii-Moriya interaction, interlayer exchange interaction, and an external magnetic field. Our results indicate that the layer degree of freedom at the surface and heterostructures provides a good platform to engineer and design the topological spin textures.