According to the fussy of evaluating index and the uncertainty of evaluating information in flight area, systems thinking tool of complex science management theory - explore graph, is used to construct the fight area risk evaluation index system. And a fight area risk early-warning model based on information entropy attribute reduction and multi-layer BP neural network is proposed. First rough set and information entropy are combined, based on information entropy attribute reduction algorithm, the reduced index information are got. Then based on the multi-layer BP network, the data collected from the flight area was intelligent reasoned and analyzed and evaluated. An example analysis by MATLAB shows that the method is feasible, and it provides support for venture investment project risk management evaluation method.