Abstract The reconstruction of past marine bottom-water redox conditions are crucial because it reflects changes in ocean circulation, surface productivity, and the precipitation–evaporation balance. However, long-term (Myr scale), high-resolution (mm scale), redox reconstructions remain scarce because traditional discrete-sample analyses are highly time-consuming. While the Japan Sea is known for past high-frequency fluctuations of deep-water redox conditions, the existing records are limited to the past 640 kyr at a relatively low resolution. In this study, we propose a novel method for estimating deep-water redox conditions using high-resolution XRF core scanning data and apply it to reconstruct Quaternary deep-water redox changes in the Japan Sea. First, we developed an XRF core scanner-based, high-throughput method that drastically accelerates the estimation of past deep-water oxygenation. We utilized XRF core scanner-derived Br/S, Fe/Ti, and Fe/S ratios, which are substitutes for the conventional redox-sensitive parameters C/S ratio, Fe/Al ratio, and degree of pyritization (DOP) respectively, for classification of deep-water redox conditions into four ranks. Then, we applied this method to a depth transect in the Japan Sea consisting of three sediment cores (~ 1000, ~2000, and ~3000 m water depths) from the Japan Sea. Our ultra high-resolution (mm scale) data reveal that deep-water redox conditions fluctuated from euxinic to oxic at ~cm scales. The depth-transect approach traces past expansion of oxygen minimum zone in some periods, which could be an analog for modern deoxygenation under global warming. Furthermore, in certain layers, redox conditions shifted progressively toward a less reducing state within centimeter-scale interval, which corresponds a few kyr. These fine scale redox changes could be detected only by using our new ITRAX-based redox rank classification method, because high-resolution sampling was difficult for conventional methods. Our new ITRAX-based redox rank classification method can be applied to other sediments obtained from different areas to advance our understanding of redox changes in the past.