In order to promote the construction of internal control in public institutions and improve work efficiency, the author proposes an optimization of internal control in public institution budget business based on random forest algorithm. We have constructed a big data audit framework for internal control of A Maritime Bureau based on the financial cloud platform and sorted out its audit process. By using the random forest algorithm to identify suspicious points in the internal control audit of administrative institutions at the data level, an example analysis is conducted using some data from A Maritime Bureau's assets, budget, revenue and expenditure, infrastructure, and contract business. The results indicate that the design of the internal control big data audit plan for administrative institutions will promote the innovation of audit information technology and application in A Maritime Bureau, provide theoretical guidance for the internal control big data audit carried out by administrative institutions, and effectively solve the problems of high workload and low work efficiency when A Maritime Bureau conducts internal control big data audits, thereby improving audit efficiency.