With the further improvement and development of Spring Boot and MongoDB technology, the solution of the enterprise has sprung up like mushrooms. But when Spring Boot integrated MongoDB database has encountered some problems, such as no complete data persistence solution. However, a review of traditional relational database has completed the work of Hibernate. This paper firstly introduces the principle and technical background of Spring Boot and MongoDB, then analyzes the existing problems of the solution. The main work of this paper is to design and implement a data persistence framework based on the solution of JPA MDBC. For example MDBC increasing and perfecting the aggregation function; provide the transaction processing and ensure data consistency; provides a backup and disaster recovery tool and so on.