The synthesis, structural characterization, and magnetic property studies of five new transition metal (M = Co, Ni) phosphonate-based cages are reported. Three substituted phenyl and benzyl phosphonate ligands [RPO3H2; R1 = p-tert-butylbenzyl, R2 = p-tert-butylphenyl, R3 = 3-chlorobenzyl] were synthesized and employed to seek out high-nuclearity cages. Complexes 1-3 are quasi-isostructural and feature a dodecanuclear metal-oxo core having the general molecular formula of [M12(μ3-OH)4 (O3PR)4(O2C(t)Bu)6 (HO2C(t)Bu)6(HCO3)6] {M = Co, Ni and R = R1 for 1 (Co12), R2 for 2, 3 (Co12, Ni12)}. The twelve metal centers are arranged at the vertices of a truncated tetrahedron in a manner similar to Keggin ion. Complex 4 is an octanuclear nickel phosphonate cage [Ni8(μ3-OH)4 (OMe)2(O3PR1)2 (O2C(t)Bu)6(HO2C(t)Bu)8], and complex 5 represents a pentadecanuclear cobalt phosphonate cage, [Co15(chp)8(chpH) (O3PR3)8(O2C(t)Bu)6], where chpH = 6-chloro-2-hydroxypyridine. Structural investigation reveals some interesting geometrical features in the molecular cores, which may provide new models in single molecular magnetic materials. Magnetic property measurements of compounds 1-5 indicate the coexistence of both antiferromagnetic and ferromagnetic interactions between magnetic centers for all cages.