The Beaufort Gyre (BG) is a key freshwater reservoir in the Arctic Ocean, and its variability could have vast impacts on global climate. Current-generation climate models (e.g., CMIP6) typically operate at coarse resolutions (~20 km) that cannot resolve boundary currents transporting Atlantic Water (AW) in the Arctic Ocean. This leads to large uncertainties in the pathways of AW and its impact on BG dynamics. Here, using an ultra-high-resolution (2 km in the Arctic Ocean) simulation of the AWI-CM3 model with substantial improvements in simulating AW inflow and boundary current structure, we demonstrate a fundamentally different BG response under warming. After excluding the influence of surface processes, we found that the resolved, intensified AW boundary currents transport more AW into the Amerasian Basin, which results in a contraction and strengthening of the BG. Our results highlight that inadequate representation of boundary currents in coarse resolution models may lead to a systematic underestimation of future BG strengthening and its climatic implications.