Planform evolution and terrestrial habitat health of two representative mid-channel bars (Baishazhou bar and Tianxingzhou bar) in the urban reach of the Middle Yangtze River in Wuhan City have not been understood under the combined influences of natural forcing and human activities. Using dry-season Landsat imagery (1989–2020), hydrological records from the Hankou gauging station (1990–2019), and field surveys, we quantified bar-morphology changes and examined the mechanisms underlying their differentiated scouring. We also developed an indicator system to evaluate terrestrial habitat health on mid-channel bars. Indicator weights were determined using a combined weighting approach integrating the Analytic Hierarchy Process and the entropy weight method. Since the Three Gorges Dam began operation, the runoff in the Wuhan reach has decreased only slightly (6.72%), whereas sediment load decreased sharply (69.88%), causing net scouring of both bars. Baishazhou bar, in a straight anabranching reach, lost 43.83% of its area (1989–2020), with erosion concentrated at the head and main channel margin and caving. Tianxingzhou bar, in a mildly curved reach, had moderate shrinkage (26.33%, 1992–2022) as revetments curbed head/right margin retreat. Both bars were “very healthy” in natural attributes, with the Baishazhou bar showing longer water–land ecotone exposure (217 d) and higher vegetation cover (92%). Socially, Baishazhou bar was “sub-healthy” due to unprotected shrinkage, and Tianxingzhou bar was “unhealthy” due to area loss and low permeability of hard works. Overall, both bars were “healthy”. These findings provide a basis for ecological conservation and habitat restoration of bar wetlands.