The relative importance of wintertime atmospheric-forced and oceanic-intrinsic SST variability in the Kuroshio-Oyashio Extension (KOE) frontal zone on submonthly timescales is evaluated based on theoretical, observational, and modelling analysis. It is shown that the local thermal coupling theoretical framework extended from the stochastic climate model has difficulties in representing observed SST variability on such short scales. We then employ the single-column General Ocean Turbulence Model (GOTM) to explicitly evaluate the SST variability forced by atmospheric disturbances. Results show that in the KOE region forced SST variability is responsible for a very small fraction of the total variability (< 10%) on the submonthly scales, indicating the dominance of intrinsic oceanic processes. Outside the KOE forced variability dominates. By means of sensitivity experiments, the key physical factors are identified: upper ocean vertical mixing, wind stress forcing (mainly for outside KOE), and latent heat flux, the former two of which are not considered in the theoretical framework. The above results are robust against different levels of submonthly SST variability. Further, to extract the intrinsic SST variability explained by mesoscale eddies, we employ an objective eddy identification and tracking algorithm together with a novel matching and filling procedure. It is found that in the Kuroshio and Oyashio frontal zone, eddy-induced SST variability is on the order of 40–60% on submonthly scales. These results highlight the different origins of submonthly SST perturbations in and outside the frontal zone, and particularly emphasize the role of mesoscale eddies and vertical mixing. The relative contribution of mesoscale and submesoscale processes to submonthly SST perturbations is open for further research.