Gentiana straminea is the famous Tibetan folk medicine thought to cure various diseases. Historically, the Qinghai-Tibetan region has been considered as the geo-authentic production area of “Mahua Jiao,” where large quantities of the medicine are grown. However, there is still little known about the phytochemical constituent spatial variation of this species. In order to find the differences between the main phytochemical constituents of G. straminea and to provide comprehensive information for quality evaluation, four main bioactive compounds (loganic acid, swertiamarin, gentiopicroside and sweroside) were analysed in 26 populations grown in areas with elevations ranging from 2320 to 4720 m across the Qinghai-Tibetan Plateau. The results showed that the four phytochemical constitutes’ concentrations varied greatly in the spatial profiling of the Qinghai-Tibetan region. Throughout the range of distribution of this species, no altitudinal, latitudinal or longitudinal trends have proven to be significant in any of the four constitutes’ concentrations or their summation. Furthermore, hierarchical clustering analysis and statistical tests showed that four populations (Liu0609-18, Liu0609-15, Liu2006-13-9 and Liu0609-22) had total constitute contents that were higher than other populations. The spatial profiling of the four phytochemical constituents suggests that the geo-authentic producing area of this species exists at a few regions within the Qinghai province, which could be attributed to specific environmental or genetic factors.