Abstract: To facilitate the intelligent transformation of traditional Chinese medicine (TCM) manufacturing, this study addresses the challenges in the honey refining process—namely, the reliance on manual experience, difficulties in quantifying multi-dimensional quality attributes, and unclear quality transfer mechanisms. This study, using real-world samples from the production of Tongren Niuhuang Qingxin Pills, established a digital measurement system for physical and chemical quality attributes of the refining process and constructed a pilot-scale quality transfer model. For physical characterization, optimized parameters were determined for dual-mode rheological testing (rotation: shear rate 50 s^-1; oscillation: frequency 5 Hz, strain 50%) to measure honey viscosity. For chemical attributes, a high-performance liquid chromatography (HPLC) method was developed to quantify pH, moisture, fructose, glucose, sucrose, maltose, and 5-hydroxymethylfurfural (5-HMF). Based on 984 data points from both atmospheric and vacuum refining processes, a kinetic model of quality transfer was constructed. The dynamic viscosity (η) showed strong correlations with moisture (S) and temperature (T) (R² > 0.998 3), effectively representing the evolution of physical properties. Additionally, the chemical kinetic model indicated that vacuum refining at low temperature, combined with honey sources low in fructose and monosaccharide/disaccharide ratios, can significantly inhibit Maillard reaction rates. This study presents a systematic digital measurement and modeling framework for the honey refining process, providing technical support for process optimization and quality consistency in TCM manufacturing under the paradigm of intelligent production.