In this study, tea saponin was used as an emulsifier to construct tea saponin-cinnamaldehyde nanoemulsion (TS-CNE) system by high-pressure homogenization nanotechnology. Preparation conditions of TS-CNE were optimized using single factor and response surface methods. The results showed that optimal TS-CNE had a particle size of 88.81 nm, a polydispersity index (PDI) of 0.113 and 86.49% retention of cinnamaldehyde. TS-CNE was stored at 4 and 25 °C for 180 days and the nanosystem was stable. Antioxidant assay showed that TS-CNE had good radicals scavenging. Furthermore, antimicrobial assay showed that the minimum fungicidal concentration (MFC) of TS-CNE was 1.95 mL/L against three pathogenic fungi (Penicillium italicum, Penicillium digitatum, and Geotrichum citri-aurantii) of citrus. TS-CNE (MFC and 10 × MFC) effectively suppressed disease development in citrus inoculated with the three fungi. Consequently, TS-CNE had good physicochemical properties and was a promising natural preservative for citrus.