Two new metal–organic frameworks (1–2) were ionothermally obtained by the reaction of a biphenyltetracarboxylic sodium (Na₄BPTC) ligand and M(OOCCH₃)₂ (M = Co(1) and Mn(2)). Crystal structure analysis reveals that 1 is a Co₃Na₆ unit-based three dimensional heterometallic MOF, while 2 exhibits a {Mn(COO)_n} chain-based three-dimensional framework. Furthermore, the magnetic measurement shows that both of them have anti-ferromagnetic properties. A combination of Density Functional Theory (DFT) and Quantum Monte Carlo (QMC) simulation uncovers that in 2 the coupling parameters between two adjacent Mn(II) ions are J₁ = −2.0 cm⁻¹ and J₂ = −1.6 cm⁻¹, and the magnetism mainly originates from the propagation of Mn(II) ions by the super-exchange of carboxylates. Interestingly, the superexchange modes of J₁ and J₂ are different. Two spin nets of −/+/− dominate in the coupling for J₁, while for J₂ there are two spin nets of −/+/− and one spin net of +/−/+.