We investigate the stability tendency of a magnetic skyrmion crystal in noncentrosymmetric tetragonal systems with the Dzyaloshinskii–Moriya interaction. We show that the stability region of the square skyrmion crystal on a square lattice depends on the Ising-type magnetic anisotropic interaction by performing the simulated annealing for the spin model. The easy-axis anisotropic interaction tends to narrow the region where the square skyrmion crystal is stabilized when the magnetic field is applied in the out-of-plane direction. In contrast, the easy-plane anisotropic interaction tends to enlarge the stability region. Meanwhile, the square skyrmion crystal induced by the easy-axis anisotropic interaction is robust compared with that induced by the easy-plane anisotropic interaction when the magnetic field is tilted from the out-of-plane to the in-plane direction. The results indicate that the instability toward the square skyrmion crystal in noncentrosymmetric crystals is sensitive to both magnetic anisotropy and magnetic fields.