Topology optimization of macroperiodic structures is traditionally realized by imposing periodic constraints on the global structure, which needs to solve a fully linear system. Therefore, it usually requires a huge computational cost and massive storage requirements with the mesh refinement. This paper presents an efficient topology optimization method for periodic structures with substructuring such that a condensed linear system is to be solved. The macrostructure is identically partitioned into a number of scale-related substructures represented by the zero contour of a level set function (LSF). Only a representative substructure is optimized for the global periodic structures. To accelerate the finite element analysis (FEA) procedure of the periodic structures, static condensation is adopted for repeated common substructures. The macrostructure with reduced number of degree of freedoms (DOFs) is obtained by assembling all the condensed substructures together. Solving a fully linear system is divided into solving a condensed linear system and parallel recovery of substructural displacement fields. The design efficiency is therefore significantly improved. With this proposed method, people can design scale-related periodic structures with a sufficiently large number of unit cells. The structural performance at a specified scale can also be calculated without any approximations. What’s more, perfect connectivity between different optimized unit cells is guaranteed. Topology optimization of periodic, layerwise periodic, and graded layerwise periodic structures are investigated to verify the efficiency and effectiveness of the presented method.