Nanoemulsion is a new multi-component drug delivery system; the selection of different oil phases can give it special physiological activity, and play the role of “medicine and pharmaceutical excipients all-in-one”. In this paper, we used glycyrrhizic acid as the natural surfactant, and Blumea balsamifera oil (BB) and tea tree oil (TTO) as the mixed oil phase, to obtain a new green functional composite nanoemulsion. Using the average particle size and polydispersion index (PDI) as the evaluation criteria, the effects of the oil ratio, oil content, glycyrrhizic acid concentration, and ultrasonic time on the nanoemulsion were systematically investigated. The stability and physicochemical properties and biological activities of BB-TTO NEs prepared via the optimum formulation were characterized. The optimal prescription was BB: TTO = 1:1, 5% oil phase, 0.7% glycyrrhizic acid, and 5 min ultrasonication time. The mean particle size, PDI, and zeta potential were 160.01 nm, 0.125, and −50.94 mV, respectively. The nanoemulsion showed non-significant changes in stability after centrifugation, dilution, and 120 days storage. These nanoemulsions were found to exhibit potential antibacterial and anti-inflammatory activities. The minimal inhibitory concentration (MIC) of BB-TTO NEs against Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa is 2975 μg/mL, 2975 μg/mL, and 5950 μg/mL, respectively. A lower level of inflammatory cell infiltration and proportion of fibrosis were found in the synovial tissue of AIA rats treated with BB-TTO NEs. These findings demonstrate that the BB-TTO NEs produced in this study have significant potential for usage in antibacterial and anti-inflammatory areas.