The Bering Strait throughflow has important implications for the Arctic freshwater, heat, and nutrients. By keeping the interannual variabilities of the atmospheric forcing only inside or outside the Arctic Ocean in numerical simulations, we can quantify their relative contributions to the interannual variability of the throughflow. We found that winds play a much more important role for the throughflow interannual variability than buoyancy forcing. Winds over the western Arctic Ocean and North Pacific determine the direction of Ekman transport, thus changing the sea surface height gradient between the two basins, and consequently influencing the volume transport strength. Although winds over the two basins are similarly important for the variance of ocean volume transport, the North Pacific winds cause stronger variability in freshwater and heat transports through modifying the inflow temperature and salinity. After 1994, winds over the western Arctic Ocean explain a larger part of the variability of Bering Strait volume transport than the winds outside the Arctic Ocean.