This article lucubrates a comprehensive and practical quality consistency evaluation method for Rong’e Yishen oral liquid (REYS) by spectral quantum fingerprints of ultraviolet (UV) and Fourier Transform Infrared Spectroscopy (FTIR), in which they were together fused with HPLC fingerprints. The similarity analyses of samples were evaluated by systematically quantified fingerprint method from the qualitative and quantitative perspectives, in which the macro qualitative similarity (S_m) and the macro quantitative similarity (P_m) were used to reflect the differences within samples. Surprisingly, there were no significant differences between the UV or FTIR spectral quantum fingerprints and their original spectra (t-test, P-value > 0.05). The correlation of them was satisfactory (Pearson’s r > 0.9220), which indicated that spectral quantum fingerprint had a good application prospect in the quantitative analyses and quality control of REYS. A fused evaluation strategy was developed in equal weights to avoid the unilaterality of a single analytical technique. The fusion results (S_m > 0.98, 91.9% ≤ P_m ≤ 106.6%) showed that 15 batches of samples were divided into grade 1 and grade 2, indicating good quality consistency. Furthermore, 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging assay was applied to study the in vitro antioxidant activity of REYS samples using Vitamin C as the positive control, and the fingerprint-efficacy relationships of spectra and HPLC for REYS samples were explored respectively with bivariate correlation analysis to give out the three-dimensional active profiling. This study illustrated that the comprehensive analysis strategy based on spectral quantum profilings and chromatographic fingerprints with antioxidant activity provides an exploratory mode for the quality consistency of TCM or herbal medicine.