The exchange flow structure was examined in the North Passage of Changjiang River Estuary, where a deep waterway project (DWP) was carried out to improve the navigability. Before the construction of the DWP, the friction effect played a significant role in shaping the transverse structure of the exchange flow. The turbulent eddy viscosity generated near the seabed can be transferred to the upper water column, which facilitated vertical momentum exchange. As a result, the landward inflow extended to −2 m below the water surface and the seaward outflow was concentrated on the shallow shoal on the southern side of the cross section. After the construction of the DWP, the turbulent mixing was suppressed as a result of density stratification. The friction felt by the water was constrained in the lower half of the water column and the vertical momentum exchange was reduced. Meanwhile, the channel became dynamically narrowed with a Kelvin number of 0.52. Therefore, the Coriolis played a minor role in shaping the transverse structure of the exchange flow. As a consequence, the exchange flow featured a vertically-sheared pattern, with outflow at the surface and inflow underneath. Additionally, the gravitational circulation was enhanced due to increase in along-channel density gradient and stratification. The exchange flow components associated with the lateral processes (residual currents induced by eddy viscosity-shear covariance and lateral advective acceleration) were reduced, which suggests that lateral processes played a minor role in modifying the along-channel dynamics when the estuary becomes dynamically-narrowed.