Spur dikes, mainly for regulating water flow and protecting river banks in the past, were found recently to have the ability to increase the fish physical habitat and improve aquatic system. However, the effect of spur dikes on aquatic system was generally ignored previously, and the studies on the influence of spur dikes on improving specific native fish physical habitat are still rare. This study reports a numerical investigation for the effects of spur dikes on the physical habitat and the minimum ecological flow in the Jinjiang River. Three spur dikes are placed along the inner bend in the study reach and two fish species of the Pelteobagrus fulvidraco and carps are selected as the target species. Two-dimensional water depth and velocity field are simulated in different discharges and the results are used to predict the corresponding weight use area (WUA). The differences of WUA before and after the building of spur dikes for the two selected fish species show that spur dikes have a significant effect on the physical habitats. And the minimum ecological flows from the instream flow increment approach are different for the two objective fish species and are also considerably impacted by spur dikes.