Researchers and winemakers have recently paid more attention to biodynamic (BDN) and organic (ORG) vineyard management to produce more healthy and regional wines. However, little attention has been paid to the correlation between agricultural systems, microbiota, and wine quality in biodynamic and organic wines in Ningxia, China. In this study, volatiles of wine and microorganism diversities during the wine fermentation using Cabernet Sauvignon grapes from vineyards of biodynamic, non-dynamics (BNDc, i.e., conventional one which was close to BND, considered to be a control of BND), organic, and non-organic (ORGc, i.e., conventional one which was close to BND, considered to be a control of ORG) in Ningxia, China were investigated. Hanseniaspora uvarum, Cladosporium sp., and Alternaria alternata were the main three fungal species, and Lactobacillus kunkeei, Citrus maxima, and Tatumella ptyseos were the main three bacterial species. Surprisingly, BDNc and ORG showed a significantly higher diversity of fungal communities than BDN and ORGc. The network in BDNc was the most complex, with the highest average degree and density and a higher clustering coefficient. Managing biodynamic and organic vineyards could result in floral, herb, spice, and medium floral aromas with low temperate fruit, tropical fruit, and berry flavors to wines. The correlation between agricultural systems, microbiota, and wine sensory systems showed that lactic acid bacteria (Lactobacillus) played critical roles in ORG and BDN by offering pleasant sensory and nutritional benefits. Moreover, Nowamyces globulus, Hanseniaspora uvarum, Lactobacillus johnsonii, Fusarium sp., Microterricola viridarii, Citrus maxima, Sphingomonas faeni, Cladosporium sp., Cladosporium ramotenellum, Cladosporium cladosporioides, Kodamaea ohmeri and Lactobacillus plantarum were positively correlated with aroma compounds. This study improves our understanding of the influence of vineyard management on microorganism succession and wine characteristics, providing a reference and scientific basis for the development of BDN and ORG wines.