Introduces a design method of intelligent controller of VAV air conditioning system based on embedded processor S3C2440A. The VAV air conditioning system adopts fuzzy PID control algorithm to real-time control room temperature. Builds a Web server by means of the embedded technology to realize remote monitoring of the air conditioning system. In the software design, runs Linux operating system, transplants graphical user interface development environment with Qtopia and Qt/E, and uses multi-process and multi-thread programming. The test results show that the whole control system has good performance.