Objective This study was designed to compare the changes in Streptococcus mutans(S. mutans) in the saliva before and after dental caries filling with resin-based composite. Methods Twenty volunteers participated in the study. The caries in the oral cavities of the volunteers were removed, and filling with resin-based composite without fluoride was performed. Non-stimulated saliva was obtained prior to treatment as well as 1, 2, 3, and 4 weeks post treatment. Approximately 100 μL of salivary sample was transferred, plated on mitis salivarius with bacitracin agar, and incubated anaerobically at 37 ℃ for 48 h. Results Compared with the number of S. mutans in the saliva prior to treatment, the number of S. mutans in the saliva 1 week after filling significantly decreased(P0.05). Conclusion The number of S. mutans in the saliva could be reduced for a certain period through caries removal and resin-based composite filling. However, the number of S. mutans in the saliva would gradually revert to its status prior to the treatment of dental caries. Relying only on the filling treatment of dental caries does not change the number of main cariogenic microorganisms in the saliva.