In recent years, bayberry decline disease has caused significant damage to the bayberry industry. In order to evaluate whether humic acid can be used to effectively control the disease, this research examined the nutritional growth and fruit quality of bayberry, soil physical and chemical properties, soil microbial community structure and metabolites. Results indicated that the application of humic acid could not only improve the vigor and fruit quality of diseased trees, but also increase the diversity of microbial communities in the rhizosphere soil. A great increase was observed in the relative abundance of bacterial genus Mycobacterium and Crossiella, fungal genus Fusarium and Coniosporium. In contrast, a significant decrease was observed in the relative abundance of bacterial genus Acidothermus, Bryobacter, Acidibacter, fungal genus of Geminibasidium and Mycena. Analysis of RDA for microbial communities and soil characteristics showed that the main four variables, including available nitrogen, phosphorus, potassium, and calcium, had a great effect on the composition of bacterial and fungal communities in bayberry rhizosphere soil at the genus level. The main four variables had a greater effect on bacterial communities than on fungal communities. In addition, ABC transporter, arginine and proline metabolism, galactose metabolism, and glutathione metabolism were significantly affected by humic acid, which changed the content of 81 metabolites including 58 significantly down-regulated metabolites such as isohexonic acid and carinitine, and 23 significantly up-regulated metabolites such as acidic acid, guaninosuccinate, lyxose, 2-monoolein, epicatechin, and pentonolactone. These metabolites also significantly correlated with rhizosphere soil microbiota at the phylum, order, and genus levels. In conclusion, the results demonstrated the role of humic acid on plant growth and fruit quality, as well as rhizosphere soil characteristics, microbiota, and secondary metabolites, which provides novel insights into control of bayberry decline disease.