Abstract To improve the data interaction control effect of a heterogeneous database and reduce packet loss rate and response time, a new heterogeneous database data interaction control system based on information fusion is designed. The system consists of hardware and software parts. The hardware part of the heterogeneous database data interaction control system is composed of a data extraction module, data sending and receiving module, encryption module, and data interaction control module. On the basis of completing hardware design, the system software is designed, a fuzzy similarity matrix is constructed by calculating the similarity among the evidence, the weight coefficient of each piece of evidence is calculated by calculating the support function of each piece of evidence, the evidence source model is modified by using discount rules, and Dempster–Shafer combination rules are transformed into matrix analysis. Combined with the modified evidence source model, information fusion of the heterogeneous database is carried out to complete the software design of the data interactive control system. The experimental results show that the data interaction control effect of the heterogeneous database in this system is good, and the packet loss rate and response time are low, improving the data interaction control effect.