In physical engineering, a rock surface, whether naturally or artificially formed, is rough. When irradiating rocks, microwaves produce reflections and diffractions on the surface of rough rocks, which significantly affect the absorption of microwave energy by rocks, thus influencing the result of microwave irradiation. In order to explore the influence of rough rock surfaces on the effect of microwave-assisted rock breaking, microwave irradiation tests were carried out on basalt samples with different values of roughness to test the temperature and P-wave velocity of the samples before and after microwave irradiation. Numerical test methods were used to systematically study the influence of rough rock surfaces on microwave irradiation. The results show that, under the same microwave irradiation conditions, the effect of microwave irradiation on rough surface basalt is more significant than that of flat surface basalt. The surface temperature distribution range of flat surface specimens is narrow, the surface temperature range of rough surface specimens is wider and more inhomogeneous, and the maximum surface temperatures of rough surface specimens are much higher than those of flat surface specimens. After irradiation, new macroscopic cracks were generated on the surface of the samples, and the crack propagation of the rough surface samples was more obvious. The decrease in P-wave velocity before and after the irradiation of flat surface samples is small, and that of rough surface samples is larger. The main factors affecting the effect of microwave irradiation on the rough surface are the refraction and reflection of electromagnetic waves, heat conduction, and stress concentration on the surface.