As one of the factors affecting the quality of honey pills (HP), there are few researches on its quality control and solutions. But water can directly affect the appearance, stability and potency of the HP. In this study, near-infrared spectroscopy was used to monitor the moisture content of HP with different drying conditions, and multiple linear regression analysis was carried out to establish the moisture content prediction model, and the R2 of the model prediction is 0.9532. The visualization of HP drying process were carried out by aquaphotomics method characterizes the status of the water molecular network at different drying stages. At the same time, low-field nuclear magnetic resonance (LF-NMR) information was carried out to analyze the water distribution in the drying process, and further verified the water solvent shell action in the water balance process of aquaphotomics analysis. The surface water of the pill disperses to the air, and the internal water diffuses outwards. We adopted the techniques such as rheology to comprehensively characterize the state of HP, and to evaluate the quality of them by using the dissolution test. The quality state of the pills was analyzed by the aquaphotomics analysis of water species. The above research system provided the scientific basis for revealing the drying process of HP from the viewpoint of aquaphotomics, as well as showed potential for expansion and application to other Chinese traditional medicine products.