In view of the destruction of ecological environment and shortage of ecological flow in the middle reaches of Fen River, we selected Lancun section and Zhaocheng section as the typical research objects to analyze the ecological flow using six hydrological and hydraulic methods, and then the rationality and guarantee rate of the calculation results were discussed. The results show that the ecological flow of the two sections had the same variation pattern, which was low in January, February and December, but high in March, and higher in flood season than that in non flood season on the whole. The interannual guarantee rate of the two sections was generally high before 1996, but decreased from 1997 to 2008, and increased with fluctuations after 2008. The guarantee rate fluctuated within the year, but the guarantee rate of Lancun section was high in March, while that of Zhaocheng section was very low. Therefore, the influence of water use of the irrigated areas and storage of reservoirs on the downstream river ecosystem should be considered. By comparing the results of the six methods, it is concluded that the monthly frequency method is not suitable for the Fen River Basin; the recommended method for the calculation of ecological flow is Tennant method for January, February and December, the Qp method for the general water use period, and the dynamic method for the flood season; in March, the wetted perimeter method is recommended for Lancun section but Tennant method for Zhaocheng section. The recommended monthly ecological flow process can reflect the change of high and low flow in different water periods of the year and provide a theoretical basis for the ecological restoration in the Fen River Basin.