Artemisiae Scopariae Herba (Chinese name Yinchen), the dried aerial part of Artemisia capillaris Thunb. (A. capillaris) or Artemisia scoparia Waldst. et Kit. (A. scoparia), is one of the most commonly used herbal drugs; the one harvested in the spring is habitually named “Mian Yinchen,” and the one harvested in the autumn is habitually named “Hua Yinchen,” but only the former is used in clinical practice in China. There are significant differences in quality between two species of A. Scopariae Herba and among A. Scopariae Herba from different harvest seasons and different producing areas, but the current comparative studies on the differences in quality of A. Scopariae Herba mainly focus on the latter; there are few comparative studies on the difference in quality between A. capillaris and A. scoparia. In this paper, the HPLC fingerprints of 13 batches of A. capillaris and 7 batches of A. scoparia harvested in spring were established, 21 common peaks in the fingerprints were demarcated, the constituents of these common peaks were identified by quadrupole‐TOF‐MS/MS, the chemical pattern recognition analysis, including hierarchical cluster analysis, principal component analysis, and orthogonal partial least squares discriminant analysis, were conducted with the quantified peak areas of common peaks as variables, and the contents of 12 constituents unambiguously confirmed by reference substances in 20 batches of A. Scopariae Herba were determined. The results showed that there exist obvious differences in quality between two species of A. Scopariae Herba, and 3,4‐dicaffeoylquinic acid, 4,5‐dicaffeoylquinic acid, 3,5‐dicaffeoylquinic acid, and chlorogenic acid can be selectively used as markers to distinguish the two species of A. Scopariae Herba.