The operation of the Three Gorges Project led to significant channel adjustments in the downstream reaches, and thus changed the diversion patterns of flow and sediment in bifurcated reaches, which had a significant impact on flood control, navigation, water diversion, and ecology. This study investigated the variation characteristics of four distinct bifurcated reaches in the reach between Jianli and Shijitou of the Middle Yangtze River. Using a two-dimensional flow-sediment transport model, this study compared the flow and sediment diversion ratios before and after the reservoir operation under different flow regimes, and consequently identified the drivers behind the variation in diversion patterns. The results demonstrate that during the post-operation period, the straight bifurcated reach underwent erosion and deposition, while both the main and second branches of the curved bifurcated reach underwent erosion, primarily occurring in the low-water channels. River regulation projects prevented the retreat of high floodplain of the mid-channel bar (MCB) and caused the deposition of low floodplain of the MCB. The channels with higher erosion intensity evolved into the main branches, causing the shift in the main and second branches of some bifurcated reaches. The low-discharge diversion ratios in the right branch of the bifurcated reaches of Nanmenzhou and Luxikou increased from 0.42 and 0.40 to 0.95 and 0.81, respectively, with both showing an increase of over 100%. The imbalanced erosion in the bifurcated reaches is the primary cause for the variation in flow and sediment diversion patterns, with the impact decreasing for a higher discharge. For every 1.0 m increase in the relative scour depth between the main and secondary branch, the flow diversion ratio of the main branch would increase by approximately 7.6–15.8%, and the sediment diversion ratio would increase by approximately 8.2–11.8%. Changes in the mid-channel bar planform would further influence the flow diversion patterns. Sediment deposition on the low floodplain was adverse to the inflow entering the left branch of the Nanyangzhou reach, while the retreat of the high floodplain in the left branch further decreased the flow diversion ratio under the medium to high discharge conditions.