An integration of medical data management system based on WEB and data mining tool is reportedly in this paper. In the application process of this system, web-based medical data mining user sends requests to the server by using client browser with http protocol, the commands are then received by the server and the server calls the data mining tools remote object for data processing, and the results are sent back to the customer browser through the http protocol and presented to the user. In order to prove the feasibility of the proposed solution, the test is done under the NET platform by using SAS and SPSS, and the detail steps are given. By the practical test, it was proved that the web-based data mining tool integration solutions proposed in this paper would have its broad prospects for development, which would open up a new route to the development of medical data mining.