The minimum instream ecological flux is referred to the one which can prevent drought out and keep the water body in existence. The computational method on the minimum water demand for ecosystem should be based on river geomorphology, and the critical flux must be determined after two facts, breakpoint on the curve of the water level with river width and maintaining the habitat to a certain extent(mainly including: average depth, average velocity, et al.), being synthetically consisdered. In this paper, on the basis of establishing the computational methodology and system based on river geomorphology, three hydrological control transects at the lower reach of the Yellow River, Huayuankou Station, Gaocun Station and Lijin Station, are chosen to check the minimum ecological flux. The computational results indicate that the minimum ecological flux of Huayuankou Station, Gaocun Station and Lijin Station is respectively 170 m~3/s, 140 m~3/s and 154 m~3/s, respectively occupying 8.9%, 7.4%, 7.9% of the natural and average flux of multi-years; the ratio of river width is respectively 35.8%, (20.6)%, 40%; average depth is respectively 0.47 m, 0.87 m, 1.02 m; velocity is respectively 0.76 m/s, 0.40 m/s, (0.81) m/s.Because the catchment area studied outside is much more smaller than the Yellow River basin, the minimum ecological flux thus is a little lower than the existed international results.