A phytochemical investigation on the fruits of Xanthium sibiricum Patrin ex Widder led to the isolation of twenty compounds. Their structures were elucidated by comparison with relevant spectroscopic data. To the best of our knowledge, compounds 3, 7, 13–15 were isolated from the family Compositae for the first time. Compounds 2, 4, 8, 20, along with compounds 11, 12, 16, 17 were firstly reported from the genus Xanthium and species X. sibiricum, respectively. Additionally, chemotaxonomic investigation revealed the close relationship between X. sibiricum and Xanthium strumarium L.