Precise control over metal-organic polyhedra (MOPs) architectures via metal and organic linker engineering presents a critical challenge for advancing functional porous materials with specific properties. The rational design of organic linkers and secondary building units (SBUs) with programmable configurational features facilitates the assembly of novel MOPs, wherein structural complexity is enhanced through the integration of low-symmetry linkers and expandable SBUs. Herein, a series of polyoxovanadate-based metal-organic polyhedra (VMOPs) with modulated structures were systematically engineered through linker desymmetrization and SBU expansion approach. Two types of tritopic triazine (D_3h)- or imidazole (C_s/C₁)-functionalized carboxylate ligands assemble with 3-connected prototype {V₆S} or expansional {V₆P} clusters, yielding VMOPs that exhibit structural evolution from T_d-symmetric regular tetrahedrons to D_2d-symmetric isosceles variants. Expansion of vertex clusters leads to structural fine-tuning of VMOPs, giving rise to diverse ligand conformations. Interestingly, these VMOPs exhibit significant differences during the iodine adsorption in both n-hexane solution and gaseous phases, which can be explained by the comprehensive influence of their cavity volume, the functional groups included, and the stacking arrangement. These findings demonstrate an effective structure-designing strategy via regulation of ligand symmetry and SBU architectural features, providing a powerful approach for the customized synthesis of MOPs with tailored structures and functionalities.