The efficient utilization of terminal area airspace and runway resource plays an important role in increasing the efficiency of air traffic flow management (ATFM). Arrival flight scheduling is one of the key parts of making use of this resource, so it is necessary to study the problem of arrival flight scheduling. Considering several influence factorsof actual sequencing processing by controllers and some factors were never considered by previous study,this paper study this problem with fuzzy comprehensive evaluation method, which could trade off the importance of each factor. But the membership function and weight number of each factor were difficult to determine. To solve this difficulty, we used rough set theory to objectively calculate weight number and combined it with fuzzy comprehensive evaluation method. In this paper, we analysearrival flight sequencing process by controllers firstly and propose five influence factors to construct index system, thenrepresent how to use this method to sequence flight and apply this method to a reality case to verify effectiveness and feasibility. The experimental result showsthat arrival-rate is improved and time of delay is decreased obviously.