ABSTRACT Artificial tiger bone powder (ATBP) is an animal‐derived traditional Chinese medicine for treating osteoporosis. The combination of NanoLC‐HRMS and UHPLC‐QQQ‐MS was used to identify and quantify the quality control markers of ATBP. Peptidomics by NanoLC‐HRMS was used to characterize the native peptides in ATBP and four individual bone extracts. Five signature peptides from the deer bone extracts were identified in ATBP and validated by comparison with synthetic peptides. These signature peptides were used as quality marker peptides to establish an analytical method using UHPLC‐QQQ‐MS, which was found to have good specificity, stability, and accuracy. The bioactivity of peptides was determined using in vitro osteoblast proliferation and anti‐inflammatory assays. GPQGIAGQRGVV and AFAQLSELH could promote the proliferation and mineralization of MC3T3E1 cells. VDVVGAEALGR and FAVEGPKLVA exhibited anti‐inflammatory effects in lipopolysaccharide‐treated RAW 264.7 cells. This strategy for screening signature peptides in ATBP exhibits significant translational potential and can be systematically applied to the identification and characterization of quality marker peptides in various animal‐derived pharmaceuticals.