Bacillus subtilis L1-21 is an endophytic bacterium to effectively inhibit citrus huanglongbing and canker disease pathogens. In order to provide theoretical basis for practical application, this study investigated the colonization dynamics and downward-conduction of B. subtilis green fluorescent labelled strain (L1-21-GFP) in citrus leaves by foliar spraying suspension with 10⁶cfu/mL. Colonization in citrus fruits was checked through spraying and soaking with 10⁸cfu/mL and control effect was evaluated on green mold by spore injection with Penicillium digitatum and incidence investigation. After 10min treatment, the colonization of B. subtilis L1-21-GFP in leaf surface and mesophyll reached 1.36×10³cfu/cm² and 8.08×10²cfu/cm², respectively, and displayed a continuous increasing trend. One hour after treatment, the GFP-tagged endophyte was stable in leaf surface with 1.51×10² cfu/cm². The bacterial concentration reached to 5.67 cfu/cm² in mesophyll after 2 h, which gradually increased to 1.15×10³cfu/cm² after 30h. Endophyte L1-21-GFP could easily colonize in fruits, and bacterial concentration in pulp and peel after 1h was 9.51×10³cfu/g and 3.51×10⁴cfu/g, respectively. However, there was significant difference in the colonization ability among fruits of different citrus varieties, and Citrus Reticulata cv Ponkan had the highest colonization. In addition, citrus green mold was successfully control on third and fifth day with 100% and 80.36% control effect, respectively, when soaked once with the bioagent for 30 min. Taken together, overall results of this study could guide us to apply B. subtilis L1-21 for field application of potential citrus diseases.