Rapid climate change-induced warming has caused significant reductions in oceanic oxygen reservoir. However, the long-term trend of oxygen in the Arctic Ocean is poorly constrained. Here we show that, during the past three decades, deoxygenation has been particularly pronounced within the Atlantic water layer at rate 4-5 times faster than other global deep waters, due to a multi-decadal reduction in oxygen solubility with the Atlantic-origin water. Conversely, deoxygenation is less significant within the Pacific winter water layer (100-300 m), despite northward expansion and thickening of low-oxygen layer, owing to increased ventilation from polynya formations. These findings highlight crucial ongoing changes to the Arctic Ocean’s oxygen cycle under interacting influences from Pacific and Atlantic inflows.