A variety of interesting modulated structures are frequently observed in composite crystals with plural subsystems, because there are mutual lattice modulations between them. By considering superspace group symmetry for quasiperiodic systems, atomic modulation functions can be applied to the structure refinement of the modulated composite crystal. By the superspace group approach, we can also understand structural interactions between substructures. A modulated structure analysis of the composite crystal with layered substructures using (3+1)-dimensional superspace groups is introduced as an example.