Rapid changes of sea ice in the Chukchi Sea are substantially influencing the marine ecosystem and carbon cycling in the region. In this study, sea ice variations during 1994–2015 are simulated with a coupled ocean and sea ice model covering the North Atlantic-North Pacific-Arctic Oceans (NAPA) with a nominal horizontal resolution of 1/4° in latitude/longitude. The model is based on version 3.6 of the Nucleus for European Modelling of the Ocean (NEMO) and version 3 of Louvain-la-Neuve Sea Ice Model (LIM). The analysis is focused on the heat budget of sea ice and sea water in the Chukchi Sea during the ice-melting season, defined as the duration with positive net water flux from sea ice to sea water. Averaged over 1994–2015, sea ice melting in the Chukchi Sea occurs from mid-May to mid-October. The relative contributions of melting at the surface and bottom of the sea ice vary spatially in relationship to the variations of sea ice concentration, in particular from June to August when the ice melts relatively rapidly. The rate of melting at the ice surface is much higher in areas with ice concentration greater than 80%, while ice bottom melting is more important elsewhere. Bottom melting accounts for 68% of the total seasonal ice loss. Further analysis of the heat budget of the sea water column reveals the contributions of net heat flux at sea water surface (including open waters, ice leads, and under ice covered areas) and Pacific inflow heat flux to ice bottom melting. First, during the entire ice-melting season, the Pacific inflow heat flux contributes ~67% of the total heat input to the sea water in the study area. Among the total heat flux input to the sea water, about 58% is used to heat the sea water, 28% is used to melt ice bottom, and 14% is transported downstream. Secondly, during the early and peak stages of ice melting (from mid-May to early August), net heat flux at sea water surface makes the dominant contribution to ice bottom melting. During the late and final stages (from mid-August to mid-October), the Pacific inflow heat flux plays a leading role and continues to provide heat during the early freezing stage, acts to slow down the freezing rate, and extends the ice-free season. Finally, ~60% of the net heat flux at ice surface is used for ice surface melting. Very little of the net heat flux at ice surface could penetrate the sea ice into the sea water for ice bottom melting. During the ice-melting season of 1994–2015, the time-mean and standard deviation of interannual variations of the following three variables in the Chukchi Sea are: (3.16 ±0.67)×1020 J for the heat content variation in the Chukchi Sea, (3.65±0.69)×1020 J for the Pacific inflow heat flux, and (1.81 ±0.46)×1020 J for the net heat flux at sea water surface. Interannual variation of heat flux causing ice bottom melting is negatively correlated with the heat content variation in the Chukchi Sea ( R =−0.62; P R =0.96; P R =1.0; P 6.06×1018 J per year, while the heat content variation in the Chukchi Sea has been increasing by 6.03×1018 J per year. Overall, the present model results suggest that variations upstream of the Pacific inflow play an important role in variations of sea ice area in the Chukchi Sea.