To understand the effects of chalcogen atoms on the crystal structure of the series of 3,7-bis(methylchalcogeno)benzo[1,2-b:4,5-b′+dichalcogenophene-based organic semiconductors, three benzodifuran derivatives (1-3) and dimethoxy derivatives of benzodithiophene and benzodiselenophene (4 and 7) were newly synthesized to complete the "3 × 3 matrix" of the oxygen-, sulfur-, and selenium-derivatives (1-9). The crystal structures of 1-9 were classified into four classes, sandwich pitched -stack (1), dimeric (2 and 3), pitched -stack (4, 5, 7, 8, 9), and brickwork structure (6 and 9). The causes for the different crystal structures depending on the chalcogen atoms were investigated by the theoretical calculations, indicating that the chalcogen atoms in the core and substituents primarily affected the packing structures. Although the crystal growth in the vapor phase afforded different polymorphs, the relationship between the crystal structure and the carrier transport property was carefully investigated. With these comprehensive evaluations, we conclude that; i) methylchalcogenolation is a powerful tool to alter the packing structure, ii) each methylchalcogeno group has its features that largely influence the intermolecular interaction and electronic structure in the solid state, and iii) organic semiconductors being crystallizable into appropriate pitched -stack structures are promising as high-performance active materials for FET applications.