Abstract: To explore the effects of microbial inoculant application on the harvest and post-harvest storage quality of cherry tomatoes and to determine the optimal fertilization method, this study applied microbial inoculants through three different fertilization methods: root drenching (Gg), foliar spraying (Ym), and root drenching+foliar spraying (GY) to cherry tomatoes during their growth stage. The study further evaluated the effects of these treatments on changes in physiological characteristics, nutritional components, and volatile flavor compounds in cherry tomatoes at harvest and during storage. The results indicated that all microbial inoculant treatments improved the fruit hardness, reduced the relative conductivity, inhibited respiration, and increased the nutritional content of cherry tomatoes. Specifically, at harvest, the total sugar content of the GY, Gg, and Ym treatments increased by 58.43%, 39.04%, and 8.8%, respectively, compared to the control (CK), while total phenol content increased by 23.5%, 11.76%, and 5.88%, and vitamin C content increased by 58.43%, 9.2%, 4.94%, and 4.14%, respectively. Additionally, the levels of volatile flavor compounds such as 6-methyl-5-hepten-2-one and trans-2-heptenal, characteristic aldehydes, were elevated, with the GY treatment showing the highest relative content. After 15 days of storage at 20 ℃ and 90% humidity, all three treatments delayed the decrease in fruit hardness. The decreases in hardness compared to harvest were 73.10%, 69.87%, 70.60%, and 69.86% for CK, Gg, Ym, and GY, respectively, and inhibited the increase in weight loss, with CK, Gg, Ym, and GY showing increases of 7.5%, 7.0%, 6.5%, and 6.4%, respectively, compared to the initial storage period. At the same time, the loss of total sugars, total phenols, and vitamin C was delayed, with the GY treatment showing higher levels of all three nutritional components compared to the other treatments. Furthermore, all treatments promoted the accumulation of key aroma and volatile flavor compounds such as 6-methyl-5-hepten-2-one and trans-2-heptenal during the later stages of storage. They also inhibited the decline of volatile flavor compounds such as 2-hexenal, trans-2-hexenal, hexanal, and the production of off-volatile flavor compounds such as acetic acid and dimethylamine. ROAV analysis indicated that hexanal (monomer), butenal (dimer), and 1-pentene-3-one were key volatile flavor compounds in cherry tomatoes, with the GY treatment showing the best results. In conclusion, the GY treatment represents the optimal method for microbial inoculant application, as it improves the overall quality of cherry tomatoes at harvest and enhances their post-harvest storage characteristics. Additionally, it promotes the accumulation of characteristic volatile flavor compounds and inhibits the production of off-flavor compounds, showing promising potential for practical application and promotion.