Rice-fish co-culture has gained increasing attention to remediate the negative environmental impacts induced by intensive aquaculture. However, the effect of rice-fish co-culture on oxygen depletion has rarely been investigated. We constructed a rice-fish co-culture system in yellow catfish (Pelteobagrus fulvidraco) and freshwater shrimp (Macrobrachium nipponense) ponds using a new high-stalk rice variety, and conducted a field experiment to investigate the effect of rice-fish co-culture on water parameters and oxygen consumption. The results showed that rice-fish co-culture reduced the nutrients (total nitrogen, ammonia-N, total phosphorous and potassium) and the dissolved oxygen content in fish and shrimp ponds. However, they showed similar seasonal change of dissolved oxygen in the water of fish and shrimp ponds. Rice-fish co-culture reduced the total amount of oxygen consumption and optimized the oxygen consumption structure in pond. The respiration rates in water and sediment were significantly reduced by 66.1% and 31.7% in the catfish pond, and 64.4% and 38.7% in the shrimp pond, respectively, by additional rice cultivation. Rice-fish co-culture decreased the proportions of respiration in sediment and water, and increased the proportion of fish respiration. These results suggest that rice-fish co-culture is an efficient way to reduce hypoxia in intensive culture pond.