In this study, we numerically investigated the rotor-stator cavity for different disk surface roughness (rough rotor-RR, rough stator-RS, and rough rotor & stator-RRS) with the aim of determining the effect of surface roughness on the heat transfer characteristics of the disk cavity over a range of parameters. First, we experimentally verified that the numerical simulation has high accuracy. Next, the third-generation vortex identification method-Ω vortex identification method is used to preliminarily analyze the effect of different disk cavity roughness on the heat transfer in the rotor-stator cavity. The results indicate that the roughness of the rotor surface plays a dominant role in influencing the flow in the disk cavity. Third, we qualitatively and quantitatively analyzed the temperature field in the disk cavity. Interestingly, we discovered that the roughness of the stator decreases the temperature in the disk cavity to some extent. Thus, we judged the effect of stator surface roughness on the flow in the disk cavity based on the pressure variation in the rotor-stator cavity and gave an optimal roughness range for the stator. This will help to improve the cooling effect in the disk cavity. Finally, we investigated the effect of roughness on the rotor-stator heat transfer capacity. The effect of roughness on overall heat transfer in disc cavities is quantified based on average local heat transfer coefficient. It was concluded that the local heat transfer coefficient of the disk cavity is sensitive to the wall roughness, even for small wall roughness. We then added a roughness term to our previous work on average Nusselt number predictions for disk cavities. This provides a more accurate prediction of the heat transfer capacity of the disk cavity. On the basis of our results, it can provide some assistance to the relevant designers to quickly and accurately predict the heat transfer capacity of the rotor-stator cavity.