Thorium monocarbide (ThC) is interesting as an alternative fertile material to be used in nuclear breeder systems and thorium molten salt reactors because of its high thermal conductivity, good irradiation performance, and wide homogeneous composition range. Here, the influence of carbon vacancy site and concentration on lattice distortions in non-stoichiometric ThC1−x (x = 0, 0.03125, 0.0625, 0.125, 0.1875, 0.25, or 0.3125) is systematically investigated using first-principle calculations by the projector augmented wave (PAW) method. The energy, mechanical parameters, and thermodynamic properties of the ThC1-x system are calculated. The results show that vacancy disordering has little influence on the total energy of the system at a constant carbon vacancy concentration using the random substitution method. As the concentration of carbon vacancies increases, significant lattice distortion occurs, leading to poor structural stability in ThC1−x systems. The changes in lattice constant and volume indicate that ThC0.75 and ThC0.96875 represent the boundaries between two-phase and single-phase regions, which is consistent with our experiments. Furthermore, the structural phase of ThC1−x (x = 0.25–0.3125) transforms from a cubic to a tetragonal structure due to its ‘over-deficient’ composition. In addition, the elastic moduli, Poisson’s ratio, Zener anisotropic factor, and Debye temperature of ThC1-x approximately exhibit a linear downward trend as x increases. The thermal expansion coefficient of ThC1−x (x = 0–0.3125) exhibits an obvious ‘size effect’ and follows the same trend at high temperatures, except for x = 0.03125. Heat capacity and Helmholtz free energy were also calculated using the Debye model; the results showed the C vacancy defect has the greatest influence on non-stoichiometric ThC1−x. Our results can serve as a theoretical basis for studying the radiation damage behavior of ThC and other thorium-based nuclear fuels in reactors.