The invention discloses a method and system for testing application compatibility of an intelligent terminal. The method comprises the steps of (1), installing an application needing testing on the intelligent terminal after an installation instruction of the application is received, and outputting installation information, (2), judging whether the application is installed successfully or not according to the installation information, and after the application is installed successfully, sending an operation instruction to the intelligent terminal and enabling the application to operate, (3), obtaining current CPU information, memory usage information and application operation screenshot information of the intelligent terminal in the operation process of the application, and sending the obtained current CPU information, the memory usage information and the application operation screenshot information to a server, and (4), carrying out data analysis on the obtained current CPU information, the memory usage information and the application operation screenshot information through the server, and displaying a test result. The method and system for testing the application compatibility of the intelligent terminal greatly relieve workloads of testing personnel, improve testing efficiency, lower testing cost and improve testing quality.