The [HPMo6O21](2-) units and carboxylate linkers can be combined to build novel polyanions by a carefully designed complementary system in self-assembly processes depending only on the number of carboxyl groups and the nature of carboxylic acids. Complexes (NH4)5[HPMo6O21(O2CC6H4OH)3]·4H2O (1), (NH4)8H2[(HPMo6O21)2(C2O4)3]·13H2O (2), (NH4)20[(HPMo6O21)4(O2CCH2CO2)6]·17H2O (3), and Cs2(NH4)10[(HPMo6O21)2(HPO3){C6H3(CO2)3}2]·5H2O (4) have been synthesized by a simple one-pot reaction of (NH4)6Mo7O24·4H2O, H3PO3, and carboxylic acid ligands in aqueous solution. Formation of these compounds is critically dependent on the identifying carboxylic acids, which play the important templated role in assembly processes. The stability of these clusters was explored using electrospray ionization mass spectrometry (ESI-MS) and (31)P NMR spectroscopy, and electron paramagnetic resonance (EPR) experiments further demonstrated the result of the interesting photochromic property.