The addition of suitable acidic organic materials to improve the soil for blueberry (Vaccinium spp.) cultivation is the foundation for ensuring the sustainable development of blueberry industry in China. However, the effects of managing orchards with different inputs of organic material to improve the soil nutrients varied substantially. To unearth the best types of organic material to improve the soil fertility for blueberry cultivation and the rates to use in their application, a cultivation experiment used rooting zone restriction container and one-year-old seedlings of highbush blueberry (Vaccinium corymbosum L. variety “Legacy”) as the test materials and pure soil as the control (CK) in this study. We compared the effects of three rates of application of pine bark and vinegar residue on the soil nutrients and microbial community structures, three concentrations of 1884, 3768, and 5652 m3 km−2 of pine bark and three of 2826, 5652, and 8478 m3 km−2 vinegar residue were designed to add to the soil, and they were designated PB1, PB2, and PB3 and VR1, VR2, and VR3, respectively. Surface soil samples were collected for analysis after the blueberry shrubs had been planted for one year. The results showed that compared with the CK, the PB1 treatment significantly increased the total potassium (TK), alkaline hydrolyzed nitrogen (AN) and available phosphorus (AP) contents in the soil. The PB2 and PB3 treatments significantly enhanced the soil organic matter (SOM), total phosphorus (TP), AN, and AP contents but significantly reduced the microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), and microbial biomass phosphorus (MBP) contents. The VR1, VR2 and VR3 treatments significantly increased the contents of soil pH, total nitrogen (TN), available potassium (AK), SOM, AN, MBC and MBP. The PB1, PB2, VR1, VR2, and VR3 treatments markedly enhanced the bacterial Shannon index. However, the VR3 treatment markedly reduced the number of fungal species and the Chao 1, ACE, Simpson, and Shannon indices when compared with those of the CK. The soil fungal diversity was more easily regulated by soil nutrients than the bacterial diversity. A redundancy analysis showed that the dominant bacterial phyla were primarily regulated by the soil AN, while the dominant fungal phyla were primarily regulated by the SOM and MBN. In conclusion, the vinegar residue was more effective than the pine bark at improving the soil nutrients. The VR2 treatment not only significantly improved the soil nutrients but also maintained the soil microbial diversity, which rendered it the best organic material to improve the cultivation of blueberry soil.