Three unusual transition-metal-monosubstituted germanomolybdates, [C3H5N2]6[GeMo11Co(H2O)O39]·9H2O (1), [C3H5N2]6[GeMo11Ni(H2O)O39]·9H2O (2), and [C3H5N2]6[GeMo11Mn(H2O)O39]·6H2O (3), have been synthesized by the reactions of transition-metal ions (Co2+, Ni2+, Mn2+) with H4[α-GeMo12O40]·14H2O in aqueous solution, isolated as the imidazole salts, and characterized by single-crystal and powder X-ray diffraction analyses, IR and UV/Vis spectrometry, cyclic voltammetry, elemental analysis, magnetic properties, and thermal gravimetric analysis. These are the first examples of transition-metal-monosubstituted germanomolybdates. The UV/Vis spectra of compounds 1–3 were recorded to investigate the influences of pH on the stability of the compounds in aqueous solution. The magnetic studies of compounds 1 and 2 indicate magnetic behavior typical of single transition-metal ions. The catalytic activity of complex 1 was also explored, and indicated its potential application in homogeneous catalysis.