Janus nanoparticles (JNPs) exhibit significant promise for enhancing oil recovery (EOR). However, their large-scale field deployment remains challenging. A key challenge lies in the insufficient understanding of how the physical characteristics of JNPs influence their transport behavior and microscopic oil displacement mechanisms in porous media. In this study, molecular dynamics (MD) simulations are employed to systematically investigate the displacement dynamics of oil trapped on rough surfaces mediated by JNPs of various geometries. The results reveal that particle shape critically affects both the pinning resistance encountered at groove edges and the accumulation patterns along lateral walls. These shape-dependent adsorption configurations in turn modulate local wettability and ultimately dictate the efficiency of oil removal from nanoscale grooves. Spherical and ellipsoidal JNPs demonstrate superior displacement performance when the groove surface is coated with a thin oil film. However, under conditions involving thick oil films, spherical JNPs exhibit limited penetration into narrow grooves due to their stable orientation at the oil–water interface, which reflects strong interfacial stability. In contrast, disc, rod, and ellipsoidal JNPs effectively disrupt thick oil films via a cooperative mechanism termed “aggregation and flipping”. Among all evaluated geometries, ellipsoidal JNPs consistently deliver optimal EOR performance across various oil film conditions. These findings provide molecular-level insights into shape-governed JNP performance in EOR, offering valuable guidance for the rational design and application of shape-optimized JNPs in oilfield operations.