We propose a systematic method to generate a complete orthonormal basis set of multipole expansion for magnetic structures in arbitrary crystal structure. The key idea is the introduction of a virtual atomic cluster of a target crystal, on which we can clearly define the magnetic configurations corresponding to symmetry-adapted multipole moments. The magnetic configurations are then mapped onto the crystal so as to preserve the magnetic point group of the multipole moments, leading to the magnetic structures classified according to the irreducible representations of crystallographic point group. We apply the present scheme to pyrhochlore and hexagonal ABO3 crystal structures, and demonstrate that the multipole expansion is useful to investigate the macroscopic responses of antiferromagnets.