Two-dimensional (2D) materials have attracted significant attention for their ability to support novel magneto-electrical transport and their optical and magnetic properties, of which their superconductivity is particularly of interest. Here we report on the behavior of superconductivity in 2D Mo2C crystals when hydrostatic pressure is applied, which has not yet been described in the literature. We found that the localization of boundary atoms disorder-induced Cooper pairs can suppress the superconducting transition temperature (Tc) as effectively as a magnetic field and current. We observed that the Tc initially decreased as the pressure increased to 1.75 GPa but then began to increase as the pressure increased further to 2.5 GPa. Our density functional theory calculations revealed that this behavior was linked to the modulation of the strength of the electron–phonon coupling and the electron property, which was triggered by compression of the lattice under high pressure. We attributed the inflection point in the hydrostatic pressure-dependent Tc curve to the structural phase transition of Mo2C from a hexagonal to an orthorhombic structure. This work presents a new avenue for the study of the superconductivity of Mo2C, which can be extended to apply to other 2D superconductors to modulate their electronic states.