Food Bioactive Small Molecule Databases (FBSMDs) provide valuable data resources for the study of molecular behavior, molecular nutrition, as well as the R&D of drugs and health products. In this review, 89 food databases were collected and 32 of them were classified as FBSMDs. Furthermore, we summarized their research contents and features in detail. It was found that most of the bioactive data of FBSMDs come from comprehensive projects and rarely from specific databases. Continuous maintenance and update are absent though most of FBSMDs function well. Compared with chemistry and biomedicine fields, there is still a lack of bioactive data of food small molecules and structured data for mining and modeling. It also reveals, due to the lack of effective integration and exploration, the application of FBSMDs is limited to some extent. We hope this study could provide new recognition for the future development of FBSMDs.