In order to solve the problems of hospital information management, such as the difficulty, the complexity of data types and the low utilization rate of hospital management data, this paper designs a hospital information management system, in view of the hospital data mining technology, this paper improves the APRIORI Algorithm and incremental decision tree algorithm to process the data and improve the utilization ratio of hospital information. The improved APRIORI algorithm is proved to be 10 times faster than the original APRIORI algorithm by designing simulation experiment scheme The classification accuracy of incremental decision tree algorithm is 5% higher than that of C4.5 Algorithm and ID3 algorithm, and the incremental learning time is less than 40% of that of C4.5 Algorithm and ID3 algorithm.