The evolution of skyrmion crystals encapsulates skyrmion's critical behaviors, such as nucleation, deformation, and annihilation. Here, we achieve a tunable evolution of artificial skyrmion crystals in nanostructured synthetic antiferromagnet multilayers, which are composed of perpendicular magnetic multilayers and nanopatterned arrays of magnetic nanodots. The out-of-plane magnetization hysteresis loops and first-order reversal curves show that the nucleation and annihilation of the artificial skyrmion can be controlled by tuning the diameter of and spacing between the nanodots. Moreover, when the bottom layer thickness increases, the annihilation of skyrmion shifts from evolving into a ferromagnetic spin texture to evolving into an antiferromagnetic spin texture. Most significantly, nonvolatile multiple states are realized at zero magnetic field via controlling the proportion of the annihilated skyrmions in the skyrmion crystal. Our results demonstrate the tunability and flexibility of the artificial skyrmion platform, providing a promising route to achieve skyrmion-based multistate devices, such as neuromorphic spintronic devices.