The Mo–C, Mo–N, and Mo–C–N systems are thermodynamically assessed based on the critical evaluation of available experimental phase diagrams, thermodynamic properties, and crystal structure data using the Calculation of Phase Diagram (CALPHAD) method. The Gibbs energy of liquid phase is described by the Modified Quasichemical Model. All solid solutions are described using the Compound Energy Formalism, considering the crystal structure of each solution phase. In particular, the presence of vacancies in both substitutional and interstitial sites of δ-Mo(C,N) (FCC_B1) phase is properly taken into account for the first time in the thermodynamic description. The present thermodynamic models with optimized model parameters significantly improve the description of the phase diagrams and thermodynamic data of the systems, compared to the previous assessments. The stability diagrams of Mo carbo-nitride system were calculated for the synthesis of nitrogen-doped Mo carbide for electrocatalyst application.