Ocean deoxygenation could potentially trigger substantial changes in the composition and reactivity of dissolved organic matter (DOM) pool, which plays an important role in the global carbon cycle. To evaluate links between DOM dynamics and oxygen availability, we investigated the DOM composition under varying levels of oxygen in a seasonally hypoxic fjord through a monthly time-series over two years. We used ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to characterize DOM on a molecular level. We find a clear trend both in diversity and molecular composition of the DOM along the oxygen gradient. As oxygen decreased, the chemodiversity was significantly increased, along with accumulation of relatively high-molecular-weight, reduced and unsaturated compounds enriched with carboxyl-group structures, which were also thermodynamically less favorable to biodegradation. Our results suggested that oxygen depletion selectively protected otherwise bioavailable compounds from decomposition and may promote the accumulation of a larger recalcitrant DOM pool in the global ocean, which could provide negative feedback to the ocean carbon sequestration and climate change.