We developed a simple and facile method for preparing two types of transition metal molybdates: AMoO₄ (A = Ni and Zn) and B₃Mo₂O₉ (B = Cu and Zn). Initially, a hydrothermal reaction at 383 K for 10 h in an aqueous solution of ammonium molybdate tetrahydrate (AMT) and metal acetates (MAc₂, M = Ni, Cu and Zn) was carried out to synthesize their precursors: NiMoO₄·xH₂O, ZnMoO₄·0.8H₂O, Cu₃(OH)₂(MoO₄)₂ and Zn₃(OH)₂(MoO₄)₂. Subsequently, AMoO₄ with a 1D structure and B₃Mo₂O₉ with a 3D structure were successfully constructed by sintering the precursors at 873 K for 3 h in air. Our result presented the first evidence that the generation of α-ZnMoO₄ and Zn₃Mo₂O₉ is dependent on the initial concentration of AMT or Zn(Ac)₂. More importantly, a highly monodisperse Cu₃Mo₂O₉ micropompon structure was successfully created by an ethylenediaminetetraacetic acid (H₄Y)-mediated hydrothermal route and a subsequent sintering process. We considered that H₄Y, a strong competitive chelating ligand, played a significant role in prohibiting the formation of the intermediate (NH₄)₂Cu(MoO₄)₂, thereby not only producing a monodisperse structure of Cu₃(OH)₂(MoO₄)₂ but also reducing the size of the structure by forming a stable complex: CuY. Three independent experiments: photocatalysis, photocurrent response and lithium storage were performed to discuss several possible applications of the as-obtained Cu₃Mo₂O₉ micropompons. Our data demonstrated that the Cu₃Mo₂O₉ material exhibited excellent photocatalytic efficiency for the degradation of Congo red under visible light irradiation. Also, the time-dependent photoresponse of the Cu₃Mo₂O₉ gave a very high ratio (about 171) of light current to dark current and a stable photocurrent density, which were a reflection of a high concentration of photogenerated electron–hole pairs. Further, the material indicated good charge–discharge stability and high coulombic efficiency in lithium-ion batteries even during the 100 cycles. We believe that the present study represents a significant step in the development of transition metal molybdates.