Keihm  made a study on the effects of the rough lunar surface on microwave brightness temperature using geometric optics (GO), which is valid only when the microwave wavelength is much smaller than the radius of curvature of the rough surface. This approach is deficient because it has no explicit wavelength dependence. The Chang'E-1 Lunar Orbiter carried out lunar microwave remote sensing of maria where the surface can be regarded as “slightly” rough, and this has motivated our study. We model the mare regolith as a multilayer planar layered media with a slightly rough top surface, and the temperature profile is retrieved by solving the heat conduction equation. The noncoherent method is utilized to calculate the emission of the multilayer media. To calculate the effect of the rough top surface on brightness temperatures, we use the bistatic transmission coefficients by applying the second-order small perturbation method. Using this model, the microwave brightness temperatures of the Apollo 12 area under different roughness conditions are calculated. It is shown that a slightly rough surface will increase or decrease the microwave radiative brightness temperature of the lunar regolith and that the change is related to the roughness, incidence angle, frequency, and polarization. In the case of measurements made by the Chang'E-1 microwave radiometer, where the incidence angle is 0°, the small-scale roughness will increase the brightness temperature of the lunar regolith.