Iris uniflora Pall. ex Link var. caricina Kitag. is a rare plant species with a limited distribution in alpine regions such as Mount Seorak and is classified as Vulnerable (VU) on the National Red List of Korea. This study focused on identifying the vegetation structure and environmental characteristics of the primary habitats of I. uniflora var. caricina to inform a systematic conservation strategy for this vulnerable species. A Braun-Blanquet vegetation survey was performed at a total of 20 sites. Vegetation classification based on species composition and analyses were conducted for importance value, nonmetric multidimensional scaling (NMS), and multi-response permutation procedure (MRPP). Vegetation was classified into three vegetation units and five species group types, and I. uniflora var. caricina exhibited high importance values in the herb layer of each vegetation unit. Furthermore, the NMS and MRPP analyses revealed that vegetation unit 1 exhibited a positive correlation with electrical conductivity (EC), species richness; vegetation unit 2 was positively correlated with altitude, soil organic matter, and exposed rock ratio; and vegetation unit 3 was positively correlated with Na+ and Mg+. Moreover, the species composition differed among vegetation units depending on the environmental conditions of the natural habitats. Therefore, it is necessary to establish conservation strategies that reflect the ecological characteristics of each vegetation unit for the systematic conservation of the species.