The dried root of Gentiana dahurica Fisch. has an intensive flavour, which suggests the presence of volatile compounds. Thus, this study aimed to develop an effective extraction method for GC–MS profiling of volatile compounds of G. dahurica. Hydro-distillation and subsequent resin enrichment (HDRE) was developed and applied to the analysis of G. dahurica in comparison with simultaneous distillation and extraction (SDE), and ultrasonic assisted dichloromethane extraction (uDCM). The major components were azulene (33.83%), 1-hexanoic acid (14.19%) and octanoic acid (11.39%) in the HDRE; octanoic acid (17.24%), nonanoic acid (13.29%) and 2,4-di-t-butylphenol (12.73%) in the SDE; and α-amyrin (25.05%), β-amyrin acetate (15.11%) and β-amyrone (4.61%) in the uDCM. Moreover, the HDRE extract was shown to have certain antimicrobial activity against four bacterial strains. Thus, the HDRE method is a promising sample preparation method for GC-MS chemical profiling of volatile components of the dried roots of medicinal plants.