To explore the effect of gravel group arrangement on the reconstruction of biological habitats and estimate the ecological flow in the reconstructed reaches, selecting Jinshaxi River in Jiangxi Province as the study area, silver carp as the study object, the optimal gravel group arrangement pattern was examined based on methods of orthogonal test design and numerical simulation, and the river ecological flow is estimated based on biological habitat method. The results indicated that flow has the most influences on the weighted usable area (WAU) of the habitat, followed by side length of the gravel accumulation body, while distance between the accumulation bodies has the least influences. The optimal gravel group arrangement type should have 20.m side length of single gravel and 9.m spacing between adjacent gravels. The WAU in the curving cut-off river channel is decreased by approximately 30% compared to that in the original river channel under bank-full discharge condition. The arrangement of optimal gravel group improves WAU by 20% compared to that in the original channel, and significantly improve the biological habitat in the curving cut-off river, with little influence on the flood discharge capacity. The basic ecological flow and the target ecological flow of the original river were 50m3/s and 718m3/s, respectively. After the reconstruction in curving cut-off river channel, the basic ecological flow and optimal ecological flow are 218m3/s and 618m3/s, respectively.