Citrus huanglongbing (HLB) is a destructive disease caused by Liberibacter species and is a serious global concern for the citrus industry. To date, there is no established strategy for control of this disease. Previously, GJ1 was screened as the biocontrol agent against HLB. In this study, two-year-old citrus infected by L. asiaticus were treated with GJ1 solution via root irrigation. In these plants, after seven irrigation treatments, the results indicated that the photosynthetic parameters, chlorophyll content, resistance-associated enzyme content and the expression of defense-related genes were significantly higher than for the plants treated with the same volume water. The content of starch and soluble sugar were significantly lower, compared to the control treatment. The parallel reaction monitoring (PRM) results revealed that treatment with GJ1 solution, the expression levels of 3 proteins with photosynthetic function were upregulated in citrus leaves. The accumulation of reactive oxygen species (ROS) in citrus leaves treated with GJ1 flag22 was significantly higher than untreated plants and induced the defense-related gene expression in citrus. Finally, surfactin was identified from the fermentation broth of GJ1 by high-performance liquid chromatography. These results indicate that GJ1 may improve the immunity of citrus by increasing the photosynthesis and enhancing the expression of the resistance-related genes.