During the past decade, research into transition-metal-substituted polyoxometalate self-assembly has been greatly developed. This review summarizes the conventional solution syntheses and hydrothermal syntheses of novel substituted polyoxometalates based on the incorporation of paramagnetic transition metals Mn, Fe, Co, Ni, and Cu, with an emphasis on the variety of nuclearities and configurations of encapsulated transition metal cores and the rich architectures of overall polyoxometalates.