Many of the world’s largest deltas are increasingly threatened by impact of climate change and human activities. The Changjiang (Yangtze River) is among the largest river, and its change of delta has received extensive attention. However, many studies covered smaller delta areas, which cannot reflect the changes of the entire delta region. Here, we present an assessment of the Changjiang (Yangtze River) mega-delta (CMD) using 60 years of bathymetric data covering the entire study area in order to gain clear insight into the comprehensive morphological changes in the Anthropocene. The net deposition rate decreased from 3.47 cm/year over the period 1954–1986 to 0.074 cm/year for the period 2005–2013 in the subaqueous-delta because of a dramatic decline in the sediment load. In particular, as the sediment load further decline due to the implementation of soil and water conservation engineering since 1980s, slight erosion occurred at a rate of −0.0019 cm/year during 1986–2002. However, the subaqueous-delta converted to a balanced state from one of slight erosion, and the depocenter moved southward between 2002 and 2013. Consequently, the morphological change of the CMD went through the following periods: fast accumulation from 1954 to 1986, and balanced accumulation/erosion during 1986–2013 (conservative state in1986–2002 and steady state in 2002–2013). Moreover, the subaerial delta of the Changjiang experienced continued progradation; the area of the subaerial delta increased from 14,857.74 km² in 1974 to 16,039.03 km² in 2013 (7.9% increase), with a net progradation rate of 29.53 km²/year; and the most pronounced progradation occurred at Chongming Island and the eastern parts of Nanhui. An important reason for these changes was land reclamation, deep-water channel projects, and shore protection, despite a marked decrease in the river sediment supply. In the future, whether the accumulation/erosion balance continues to be maintained will be an urgent research in the CMD.