Layered quantum materials can host interesting properties, including magnetic and topological, for which enormous computational predictions have been done. Their thermodynamic stability is much less visited computationally, which however determines the existence of materials and can be used to guide experimental synthesis. MnBi2Te4 is one of such layered quantum materials that was predicted to be an intrinsic antiferromagnetic topological insulator, and later experimentally realized but in a thermodynamically metastable state. Here, using a combined first-principles-based approach that considers lattice, charge, and spin degrees of freedom, we investigate the metastability of MnBi2Te4 by calculating the Helmholtz free energy for the reaction Bi2Te3 + MnTe → MnBi2Te4. We identify a temperature range (~500–873 K) in which the compound is stable with respect to the competing binary phases, consistent with experimental observation. We validate the predictions by comparing the calculated specific heats contributed from different degrees of freedom with experimental results. Our findings indicate that the degrees of freedom responsible for the van der Waals interaction, lattice vibration, magnetic coupling, and nontrivial band topology in MnBi2Te4 not only enable emergent phenomena but also play a crucial role in determining its thermodynamic stability. This conclusion lays the foundation for the future computational material synthesis of novel layered systems.