The present study was designed to establish a comprehensive and practical method for the quality evaluation and control of herbal preparation (HEP). The chemical information of belamcandae rhizoma antiviral injection (BRAI) was extracted using a dual-system control system comprised of HPLC chromatography and attenuated total reflection Fourier transform infrared (ATR-FT-IR) spectroscopy. To begin with, a quantitative analysis of six BRAI index components was accomplished. On this basis, HPLC five-wavelength fusion fingerprint was established to control the overall quality of BRAI. Secondly, the quality control system of ATR-FT-IR spectroscopy was constructed, that is, a quantitative analytic model to forecast the total amount of index components. Concurrently, the ATR-FT-IR quantized fingerprint was established for similarity analysis utilizing the Systematic quantified fingerprint method (SQFM). In addition, an integrated evaluation technique based on equal weights was presented to assure the comprehensiveness of chemical information. The 20 samples demonstrated good consistency in terms of quality, with a quality rating of grade 1–3. Notably, the rationality of the average method of Systematic quantified fingerprint method application in BRAI was further verified using PCA and low-level data fusion. Finally, this paper developed a model for intelligent analysis that is both quick and complete. We have redefined the quality standard of belamcandae rhizoma that can be put into production (70%< P_m<130%) in light of the influence of other HEM in the BRAI. This research demonstrated a quality analysis technique based on chromatography and spectrum, which was suited for HEP consistency control since it was easy, quick, accurate, and reliable.