Time series analysis of overwintering cereals in snowy areas has revealed several phenological patterns associated with climate changes in winter. Herein, to investigate the recent effect of climatic variations on overwintering cereals, we investigated the phenology over multiple decades at three snowy region sites with an air temperature (Tair) increase trend of 0.48–1.09 °C/decade. Our findings were as follows: heading trends differed within the same cultivar at different sites; phenology was promoted with increasing temperatures in cooler regions and decreasing snow duration in regions with heavy snow; crown temperature (Tcrown) was a more direct determinant than Tair in phenology estimation model in regions with heavy snow. A thermal gap of more than a few degrees Celsius between Tair and Tcrown, owing to the insulation effect of snowpack, affected the phenology of overwintering cereals. A shorter snow cover period promoted phenology in locations with temperatures >0 °C. Subsequently, we found that when the thermal gap was >0 °C of the growing temperature range, Tcrown directly helped determine the phenology of overwintering cereals, and irrespective of the warming trend, the periodic inflow of cold air into the northern mid-latitudes of the Northern Hemisphere and associated snow cover changes dominated Tcrown, resulting in annual phenological anomalies with a range of fluctuations of approximately 1 month. The trend of increasing Tair during spring in northern Japan is consistent with the global trend, with a pronounced trend of advancing phenology reaching >4 days/decade in a typical cooler location experiencing snowmelt in March.