This study investigates the climatology and physical factors governing the precipitation efficiency of Atmospheric Rivers (ARs) landfalling in Japan. Using an ERA5 reanalysis-based AR database (1940–2023), we identified typical synoptic patterns of landfalling ARs via Self-Organizing Maps, which effectively categorize the regional moisture transport pathways. Climatological analysis revealed a significant increasing trend in AR frequency specifically in northern Japan. We further examined the relationship between AR characteristics and rainfall using nationwide high-resolution observations. While Integrated Water Vapor Transport (IVT) explains a substantial portion of the overall relationship (R = 0.71), considerable variability in precipitation amounts remains for similar IVT levels. Our analysis demonstrates that rainfall intensity is primarily modulated by a combination of strong moisture convergence (MVIMC), low convective inhibition (CIN), and orographic enhancement over high elevations. Furthermore, precipitable water (PW) emerged as the critical differentiator for the formation of quasi-stationary linear rainbands (QSLRBs), which consistently develop in close proximity to the AR axis. These findings suggest that the synoptic-scale AR provides the necessary environmental conditions for the organization of mesoscale extremes. Enhancing the predictive accuracy of AR landfall location and internal structure is thus a crucial prerequisite for improving the predictability of catastrophic localized rainfall in East Asia.