We explore magnetic field effects on the nuclear matter based on the skrymion crystal approach for the first time. It is found that the magnetic effect plays the role of a catalyzer for the topological phase transition (topological deformation for the skyrmion crystal configuration from the skrymion phase to half-skyrmion phase). Furthermore, we observe that in the presence of the magnetic field, the inhomogeneous chiral condensate persists both in the skyrmion and half-skyrmion phases. Explicitly, as the strength of magnetic field gets larger, the inhomogeneous chiral condensate in the skyrmion phase tends to be drastically localized, while in the half-skyrmion phase the inhomogeneity configuration is hardly affected. It also turns out that a large magnetic effect in a low density region distorts the baryon shape to an elliptic form but the crystal structure is intact. However, in a high density region, the crystal structure is strongly effected by the strong magnetic field. A possible correlation between the chiral inhomogeneity and the deformation of the skrymion configuration is also addressed. The results obtained in this paper might be realized in the deep interior of compact stars.