Deltaic channels are key pathways connecting rivers and the ocean, which is of significance for in maintaining estuarine stability and material transport processes between land and sea. However, deltaic channels have experienced dramatic variations in the Anthropocene era, including seriously scouring induced by decline of riverine sediment delivered to the ocean, trenching caused by dredged works and episodic filling by storm events. Here, a series of hydrology, sediment as well as elevation data between 1979 and 2020 of North Passage (NP), one of most important navigated channels over the Changjiang Estuary Delta, were used to analyze its long-term morphodynamic processes. Results show that during 1979–2020, NP capacity presented stage changes: gentle increase stage between 1979 and 1997, fluctuation stage between 1997 and 2002, fast-descend stage between 2002 and 2007, slow growth stage between 2007 and 2020, and periodic signals of 13 and 25 months can be detected in NP volume. Meanwhile, the shoal zone and the deep channel showed long-term decrease and increase trend respectively, making NP turn into a narrow and deep deltaic channel. Moreover, NP exhibited two major morphodynamic patterns. The first mode indicates the long-term continuous erosion of the main-channel region and persistent deposition in the groin region. The second mode explains the transition of the erosion/deposition state of NP, where the huge mouth bar system in NP was shifted seaward accompanied by a decrease of its extent. The periodic changes of fluvial water and sediment may contribute the oscillation of erosion and accretion process of NP. The construction of engineering structures and long-term dredging works resulted in constant deposition in the groin region with continuous erosion in main-channel region. The existence of estuarine turbidity maximum was conductive to deposition in the main-channel region.