In order to make a decision about a region's current warning status of Citrus bacteria canker disease so as to guide farmers to take several effective measures to prevent and control it, a web-based automatic warning system for Citrus bacteria canker disease using AHP is proposed in this paper. For current factors which could cause Citrus bacteria canker disease are diversity, dynamic, real-time changes and etc. we use AHP methodology to take different factors into consideration and change the factors and their impacts whenever needed. Once each factor's weight is calculated, combing with a region's actual situation about these factors, we can obtain the region's current warning status by multiplication. Thus we can take several corresponding measures to prevent and control it. The application of this system shows that the design of the proposed multi-factor automatic warning system for citrus bacteria canker disease has been validated and we can get each factor's weight easily by using AHP. The system could help user to make objective judgments on subjective descriptions and get the correct result about a region's current warning status finally.