In this paper, the effect of different surface roughness and temperature on molybdenum's emissivity was studied. We measured and analyzed the emissivity of molybdenum with surface roughness ranging from 5 to 103 nm at 25, 600, 800, and 1030 °C. The emissivity of molybdenum increases with the temperature and surface roughness. For molybdenum with a flat surface, the emissivity is relatively low within the temperature range of 600–1000 ℃, with an average emissivity of less than 0.1. Whereas for samples with large roughness, the average emissivity is greater than 0.1 and changes significantly with temperature. Considering the cutoff wavelength of 2.2 μm for InGaAs cell, the proportion of the spectrum emitted by the samples at 600 ℃ in the 1–2.2 μm is around 10 %. At 1030 °C, the proportion reaches 44.1 % for the flat molybdenum and gradually declines with the surface roughness. Moreover, the effect of the surface roughness of molybdenum on the radioisotope thermophotovoltaic (RTPV) system was analyzed. The results show that a molybdenum emitter with larger roughness can improve the conversion efficiency of the RTPV system.