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Micro-Raman spectroscopy has become an important tool in probing thermophysical properties in functional materials. Localized heating by the focused Raman excitation laser beam can produce both stress and local nonequilibrium phonons in the material. Here, we investigate the effects of hot optical phonons in the Raman spectra of molybdenum disulfide and distinguish them from those caused by thermally induced compressive stress, which causes a Raman frequency blue shift. We use a thermomechanical analysis to correct for this stress effect in the equivalent lattice temperature extracted from the measured Raman peak shift. When the heating Gaussian laser beam is reduced to 0.71  μm, the corrected peak shift temperature rise is 17% and 8%, respectively, higher than those determined from the measured peak shift and linewidth without the stress correction, and 32% smaller than the optical phonon temperature rise obtained from the anti-Stokes to Stokes intensity ratio. This nonequilibrium between the hot optical phonons and the lattice vanishes as the beam width increases to 1.53 μm. Much less pronounced than those reported in prior micro-Raman measurements of suspended graphene, this observed hot phonon behavior agrees with a first-principles based multitemperature model of overpopulated zone-center optical phonons compared to other optical phonons in the Brillouin zone and acoustic phonons of this prototypical transition metal dichalcogenide. The findings provide detailed insight into the energy relaxation processes in this emerging electronic and optoelectronic material and clarify an important question in micro-Raman measurements of thermal transport in this and other two-dimensional materials.