CO2 displacement has emerged as a promising technique for enhancing shale oil recovery, making it crucial to understand how CO2 behaves in the nanometer-scale pores of shale. This knowledge is vital for developing effective CO2 injection strategies. In this study, we employed direct numerical simulation to investigate the impact of rough surfaces on CO2 displacement within the tiny pores of shale formations. Our objective was to elucidate how surface roughness and morphology influence the displacement process by quantifying CO2 movement in rough nanochannels. Taking into account the slip effect, we examined the CO2 displacement process across three types of channel models. Our research revealed that in single channels, rough surfaces significantly reduce the displacement paths available to CO2, thereby slowing down the overall displacement rate. Additionally, periodic fluctuations at the interface further obstruct the CO2 displacement process. The results from our simulations underscore that the surface roughness of shale nanometer pores plays a critical role in CO2 displacement, leading to non-negligible effects. These findings highlight the importance of considering surface roughness and slip effect in the design and optimization of CO2 injection techniques for improved shale oil recovery.