By introducing the flexible ligands into the molybdate system, 12 novel isopolymolybdate frameworks based on four types of [Mo8O26](4-) isomers (theta, beta, gamma, and delta) and one kind of [Mo3O10](2-) polyoxcanion were obtained. Structural analyses indicate that, during the self-assembly and crystallization process, the change of metal ions and ligands can result in the formation of different peripheral cluster environments which promote the kinetic preference of one isomeric form over another or both.