Volatile compounds are important components of the flavor quality of Chinese chives, but the distribution of flavor components in different organs of Chinese chives is still unclear. In this experiment, two Chinese chive varieties, ‘Fu Jiu Bao F1’ and ‘Jiu Xing 22’, were taken as test materials, and the contents of volatile compounds in different stages and organs of Chinese chive were determined by HS-SPME/GC-MS technology. A total of 70 and 85 volatile organic compounds (VOCs) were detected in various organs of two varieties at the commodity harvesting stage and physiological maturity stage, respectively. The total volatile compound content of Fu Jiu Bao F1 in the stage of commodity harvesting was higher than that of the physiological maturity stage, but Jiu Xing 22 showed the opposite trend. The organ distribution pattern of total volatile compounds in Fu Jiu Bao F1 and Jiu Xing 22 at the commodity harvesting stage was consistent, as follows: leaf > pseudostem > root. However, at the physiological maturity stage, the distribution pattern of Fu Jiu Bao F1 was different from that of Jiu Xing 22. Further, sulfur-containing compounds at different stages showed different organic distributions. Comprehensive analysis indicated that organic-common and organic-specific compounds varied from different cultivars and growth stages of Chinese chive, and organ differences in VOC distribution were greater than the varieties’ differences based on PCA analysis. The results of this study clarify the composition and organ distribution of volatile compounds in Chinese chive and provide a direction for the study of Chinese chive flavor quality.