Heracleum persicum Desf. ex Fischer seeds are a rich source of essential oils (EOs) with high antimicrobial and antioxidant effects. In order to determine the phytochemical variability in various Iranian H. persicum populations, seed samples were collected from 10 different climatic locations. The current study indicated that hexyl butyrate (20.9–44.7%), octyl acetate (11.2–20.3%), hexyl-2-methylbutyrate (4.81–8.64%), and octyl 2-methyl butyrate (3.41–8.91%) were the major components of the EOs. The maximum (44.7%) and the minimum (20.9%) content of hexyl butyrate were obtained from Kaleibar and Sari populations, respectively. Moreover, the octyl acetate content ranged from 2% (in Mahdasht) to 20.3% in Torghabeh population. The CA and PCA analysis divided the 10 Iranian H. persicum populations into three major groups. Populations from Khanghah, Kaleibar, Shebeilo, Showt, Mahdasht, and Amin Abbad showed a distinct separation in comparison with the other populations, having high contents of hexyl butyrate (39.8%) and low contents of octyl acetate (13.5%) (Chemotype II). According to correlation analysis, the highest correlation coefficient was among habitat elevation and hexyl butyrate content. In addition, the mean annual precipitation was negatively correlated with the content of hexyl butyrate. Although octyl acetate content showed high correlation with soil EC and mean annual temperature, it was not statistically significant. In general, in order to have plants with a high content of hexyl butyrate, it is recommended to harvest these plants from regions with high altitude and low rainfall such as Kaleibar.