Wuyi Rock Tea (WRT) is cherished for its exceptional “rock flavor” and its quality shows obvious regional differences. However, the flavor characteristics of Primary Wuyi Rock Teas (PWRTs) from different production areas remain unclear. Here, the Camellia sinensis var. sinensis cv. ‘Rougui’ and ‘Shuixian’, two quintessential cultivars for making WRT, planted in Zhengyan, Banyan, at high elevations, and Waishan production areas were used to make PWRTs. We conducted a comprehensive comparison of the sensory attributes, volatile organic compounds (VOCs), and macro-compositions of PWRTs of ‘Rougui’ and ‘Shuixian’ cultivars from different producing areas. Sensory evaluation indicated that both ‘Rougui’ and ‘Shuixian’ PWRTs from Zhengyan exhibited the best flavor qualities, followed by those from Banyan, at high altitudes, and Waishan production areas. The results of the determination and analysis of VOCs showed 680 VOCs in ‘Rougui’ and ‘Shuixian’ PWRTs, and that the different production areas mainly influenced the quantitative pattern of VOCs and rarely the qualitative composition. Integrated multivariate statistical analysis methods revealed that benzyl alcohol, hotrienol, butanoic acid, 2-methyl-, hexyl ester, benzene, (2-nitroethyl)-, and geranyl isobutyrate may be the key VOCs affecting the aroma differences in PWRTs from different production areas. In addition, water-extractable substances, tea polyphenols, caffeine, and free amino acids may be the important macro-compositions that distinguish PWRTs from different production areas. The metabolite basis for differences in the flavor qualities of PWRTs across production areas was elucidated, which may be helpful for the production of high-quality WRT.