In this study, we investigate the stability of a magnetic skyrmion crystal with short-period magnetic modulations in a centrosymmetric body-centered tetragonal system. By performing the simulated annealing for the spin model, incorporating the effects of the biquadratic interaction and high-harmonic wave–vector interaction in momentum space, we find that the double-Q square skyrmion crystal consisting of two spin density waves is stabilized in an external magnetic field. We also show that double-Q states appear in both low- and high-field regions; the low-field spin configuration is characterized by an anisotropic double-Q modulation consisting of a superposition of the spiral wave and sinusoidal wave, while the high-field spin configuration is characterized by an isotropic double-Q modulation consisting of a superposition of two sinusoidal waves. Furthermore, we show that the obtained multiple-Q instabilities can be realized for various ordering wave vectors. The results provide the possibility of realizing the short-period skyrmion crystals under the body-centered tetragonal lattice structure.