Since the impoundment of the Three Gorges Reservoir (TGR) and the joint regulation of upstream cascade reservoirs, the sediment transport environment of the TGR, particularly within the variable backwater zone, has undergone significant changes. As a sensitive reach subject to alternating river–reservoir influences, the evolution of suspended sediment vertical distribution in this zone directly affects sediment management strategies at the reservoir tail and navigational maintenance. Based on long-term field observations from 2009 to 2020, this study systematically identifies suspended sediment vertical distribution patterns in the variable backwater zone using the K-means clustering algorithm and quantitatively evaluates the applicability of the classical Rouse equation and the Han Qiangwei non-equilibrium sediment transport formula. A total of 267 measured vertical profiles are classified into three typical patterns: low-concentration weak-gradient pattern (Pattern 0, 67.8%), medium-concentration positive-gradient pattern (Pattern 1, 28.8%), and high-concentration quasi-uniform pattern (Pattern 2, 3.4%). The results reveal pronounced temporal differentiation among the distribution patterns. On the intra-annual scale, the patterns are closely associated with flood-season hydrological processes: Pattern 0 predominates during the pre- and post-flood periods, whereas the other patterns mainly occur during the main flood season (July–August). On the interannual scale, the low-concentration pattern increased steadily during 2009–2020 and became the dominant distribution in the variable backwater zone after 2014 under cascade reservoir regulation. This evolution is consistent with the intensified clear-water release effect induced by the operation of the TGR and the Jinsha River cascade reservoirs, indicating a persistent non-equilibrium sediment transport regime in which sediment transport capacity substantially exceeds sediment supply. In terms of formula performance, the Rouse equation and the Han formula yield comparable results for calculating depth-averaged suspended sediment concentration. However, for unit-width sediment discharge, the Han formula effectively corrects the systematic underestimation under Pattern 0 by introducing a non-equilibrium coefficient, showing significantly higher accuracy and stability than the Rouse equation. Both formulas exhibit limited capability in representing near-bed high-concentration layers. Future studies should focus on improving diffusion coefficient parameterization under unsteady flow conditions in variable backwater zones and incorporating fine-sediment flocculation processes to enhance sediment transport predictions under complex hydraulic conditions. The findings provide important theoretical support for understanding sediment transport mechanisms and optimizing regulation strategies in variable backwater zones of large reservoirs.