Cinobufacini injection, prepared from the skin of Bufo bufo gargarizans Cantor, has presented its significant effects on the treatment of hepatitis and various cancers in the clinic. However, as an unclear complex chemical system, the optimization of its quality control markers has been a long-term challenge. In present study, a feasible strategy integrated markers screening, determination, and statistical analysis was efficiently proposed, especially for the undefined Chinese medicine injections. First, rapid separation LC-quadrupole-TOF-MS method was applied in the identification of 19 major compounds in the cinobufacini injection for the first time. Further, nine high-level contents active compounds were selected as quality control markers for the quantification analysis. An acceptable and validated determination method was established in 17 batches of cinobufacini injection by HPLC-photodiode array detection method, including linear regression relationship (r2, 0.9996–1), precisions (RSD, 0.02–1.35%), repeatability (RSD, 0.05–1.97%), stability (RSD, 0.1–3.85%), and recovery (95.88–104.89%). Each analyte was detected at its maximum ultraviolet spectra wavelength. Finally, based on the quantification results, principal component analysis was performed on the quality assessment of cinobufacini injections. This three-step strategy provides a newly feasible solution for the quality control of Chinese medicine injections.