In order to assess flood losses accurately and rapidly, the author has developed the assessment system of flood losses for Poyang Lake area based on GIS. Firstly, the author has established the assessment model of flood losses for Poyang Lake area, which contains building flood hazard database, selecting flood hazard factors, improving neural network training model, verifying analysis, etc. Secondly, the author has designed the system structure, which includes six sub-system, water regime acquisition, flood forecasting, information inquiry, assessment of flood losses, flood scheduling and system settings. Then the assessment system of flood losses has been developed by using Visual Basic 6.0 and MATLAB in Arc Engine. Finally, the system has been applied in the Poyang Lake area, and the application result shows that the assessment system of flood losses has good feasibility and practicality.