The increasing hypoxia off the Changjiang Estuary has received intensive attractions, while less knowledge is obtained due to lack of systematic long-term observations. The repeated surveyed data of the transect from the Changjiang Estuary to the Cheju Island in the summer from 1997 to 2014 were collected and revealed a dual core of hypoxia distribution feature, namely the nearshore core and the offshore core in the northern estuary. The location of nearshore core was close to the river mouth and stable, where the hypoxia became more serious with the lowest DO descending at a rate of 0.07 mg/L/year and the thickness of hypoxia rising at a rate of 0.32m/year. The location of offshore core is around 40-m isobath but moved back and forth between 123.5–125°E with large fluctuation of minimum DO concentration and the thickness falling at a rate of -1.71m/year. The potential factors affecting the minimum DO concentration in the two cores varied as well. In the nearshore core, the decreasing lowest DO was driven by the increase of stratification and primary productivity. The enhanced extension of the Changjiang Diluted Water (CDW) strengthened stratification, and the enhanced intrusion of the Taiwan Warm Current (TWC) brought in more low DO water. In the offshore core, the fluctuating trend of the minimum DO concentration shows that both DO loss and DO supplement are distinctive. The DO loss is primarily attributed to bottom apparent oxygen utilization caused by the organic matter decay and also relevant to the advection of low DO from the nearshore core. The DO supplement is primarily attributable to weakening stratification. Analyzed results suggested large inter-annual variability for the hypoxic zone migration. The extremely low minimum DO concentration in 1998, 2003, 2007 and 2010 is the reason that the confidence of the descending minimum DO in nearshore cores is lower than 95%.