Bone collagen peptides prepared by enzymatic hydrolysis are mixed peptides with a variety of potential biological activities. However, there is a lack of research on targeted screening of bone collagen peptides with the ability to promote osteoblast proliferation. In this study, the molecular mass and sequence of yak bone collagen peptides prepared by enzymatic hydrolysis were determined by high performance liquid chromatography (HPLC) and nano-liquid chromatography-tandem mass spectrometry (nano LC-MS/MS), respectively. The semi-flexible docking method CDOCKER based on epidermal growth factor receptor (EGFR) was used for the targeted screening of bone collagen peptides with the ability to promote osteoblast proliferation. Finally, in vitro cell tests were used to verify the molecular docking results. Results indicated that a total of 78 yak bone collagen peptides were identified, the low-molecular-mass ones being predominant (those with molecular mass less than 3000 Da accounted for 91.8%). GPAGPQGPRGDKGETGEQ (GP-18, 1736.815 Da), TPEVDDEALEKFDK (TP-14, 1634.775 Da), GPAGPQGPRGDKGETGE (GP-17, 1608.757 Da), GKSGDRGETGPAGPAGPIGPV (GK-21, 1875.951 Da), and GKSGDRGETGPAGPAGPIGPVG (GK-22, 1932.973 Da) had the potential to promote osteoblast proliferation. The relative proliferation rate of mouse MC3T3-E1 osteoblasts treated with 3.0 mg/mL GK-22 was 106%, which was significantly higher than that of the control group (P < 0.05). The results of this study provide a theoretical reference for targeted screening and industrial preparation of bioactive peptides with the ability to promote osteoblast proliferation.