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Native microorganisms on wine grape surface contribute to regional wine characteristics and quality. The Xinjiang Uygur Autonomous Region in northwest China is one of the eight main wine-producing areas in China. To investigate the relationship between the microbial community structure of wine grape epidermises and environmental conditions, 16S rDNA and ITS sequences of 48 wine grape samples from four wine grape cultivars and six wine-growing regions in Xinjiang were sequenced, based on Illumina high-throughput sequencing technology. A total of 691 operational taxonomic units (OTUs) in 16 bacterial phyla and 349 OTUs in three fungal phyla were identified. Among them, Proteobacteria and Ascomycota were the predominant bacteria and fungi, respectively. Canonical correspondence analysis indicated that bacterial community diversity was largely related to altitude, latitude and longitude, while that of the fungi was closely related to altitude, dryness, frost-free period, latitude and longitude. Our results suggest that microbial community structure on the surface of wine grape is controlled primarily by geographical conditions.