The e-business-based alliance is an advanced organization form and receives much concern at home and abroad. The issue on alliance e-business security threatens alliance normal operation, so the research on the evaluation of alliance e-business security is important. According to the connotation and research contents of alliance e-business security, the study designs the evaluation method. Applying to BP neural network, the study scientifically establishes the evaluation system of alliance e-business security basing on the analysis of alliance macroeconomic environment and internal environment research. Through empirical research, the study analyses the existing situation of manufacturing industry alliance e-business security and provides suggestions for reference to solve the issue on alliance e-business security.