Three surfactant-encapsulated polyoxometalate (SEP) complexes were synthesized by grafting T-shaped quaternary ammonium units onto the surface of K5BW12O40, K6SiW11O39Co, and Na10[Mn4(H2O)2(VW9O34)2]·34H2O. All the complexes possess shell–core structures, in which the peripheral mesogenic units adopt a lateral attachment. The bulk organization of the complexes with thermal stimulus was studied by polarized optical microscopy, differential scanning calorimetry, and X-ray diffraction. The quaternary ammonium surfactant alone was found to form smectic structures, whereas the SEPs exhibited nematic characteristics. The detailed structural characterizations suggested the presence of a delicate synergy between the surfactants and polyoxometalates (POMs). The orientation of the mesogenic units was demonstrated to have a pivotal influence on the formation of liquid crystalline structures of the SEPs by comparison with the reported SEPs with head-to-tail attached mesogenic units. The clearing temperatures of the nematic complexes were found to be dependent on the number of peripheral surfactants. Finally, the magnetism of the polyoxometalates was proven to be well maintained in the liquid crystalline matrices, which allows the potential development of magnetically tunable liquid crystals bearing nematic structures.