Blueberry has high nutritional value and is favored by consumers, so the planting area is increasing. However, due to the influence of climate conditions and the edaphic environment, achieving high production and the healthy growth of blueberries has become a major problem. In this study, we collected soil and blueberry plants which had normal and limited growth to determine the underlying causes of poor growth by characterizing soil pH, EC, enzyme activities and the microbiome, plant growth properties, and root metabolites. The results showed that the pH of the blueberry rhizosphere soil was less than 6.0 in the case of plants growing well, and higher than 6.0 in case of plants growing poorly. The activities of acid phosphatase and invertase were significantly higher in the rhizosphere soil of the normally growing than growth-limited blueberry plants. The relative abundance of Proteobacteria and Saccharibacteria was higher in the rhizosphere soil of normally growing than growth-limited blueberry plants and they were positively correlated with activity of soil acid phosphatase. Ascomycota, as the dominant fungi, had the highest relative abundance in the rhizosphere soil of growth-limited blueberry plants. The six metabolites showing enrichment in the KEGG pathway analysis were thymidine, cholic acid, raffinose, p-salicylic acid, astaxanthin, and inosine. It was found that flavonoids were correlated positively with soil fungi abundance. The contents of flavonoids apin, rutin and epigallocatechin were significantly higher in roots of growth-limited than normally growing blueberry plants. The content of the flavonoid daidzin was significantly higher in the roots of poorly growing blueberries compared to normally growing ones. In conclusion, the growth of blueberry was significantly related to soil organic matter, soil enzyme activity and soil microbial community diversity.