With the deepening of digital development, the security protection of databases becomes more important while carrying out the digital transformation of party-building work in colleges and universities. In this study, for the database security in the party building work in colleges and universities, the protection framework of database security protection and the database hierarchical protection system based on the party building work in colleges and universities are constructed according to the needs of data hierarchical security protection. Then, on the basis of the intrusion tolerance mechanism, a database security monitoring system is established using a voting algorithm, and a multilevel information access control method is proposed for hierarchical protection. On this basis, an encryption protection mechanism based on the RSA algorithm is proposed for the sensitive information in the database of university party-building work. Through the empirical analysis of the security mechanism of counterattack protection of the university party building database, it is known that the security of the system in this paper and the probability of normal operation are both greater than 99%, and the likelihood of danger is 0.000002%. In the application of party building work, the data security of the three kinds of business is still maintained above 99.6%. The encryption time consumed is not more than 525ms, which shows that the database hierarchical protection security mechanism system constructed in this paper can meet the requirements of database security in the party building work in colleges and universities and provide a reliable guarantee for the security of the party building work database.