Hyaluronic acid (HA), a polysaccharide, is widely used for its essential physiological functions. Although the structures of low molecular weight HA produced by both acid and enzyme degradation methods are extremely similar, there are still differences due to the different degradation principles. There is currently no clear way to distinguish between HA prepared by acidolysis and enzymatic hydrolysis. Based on near-infrared (NIR) spectroscopy and aquaphotomics technology, a method for distinguishing HA raw materials and their mixtures from different sources was proposed, and HA with different mixed ratios was accurately quantified. First, NIR spectra of the HA samples were collected. The spectra were then preprocessed to improve the spectral resolution. Spectral information was extracted based on wavelet transform and principal component analysis, resulting in a final selection of 12 characteristic wavelengths containing classification information. The discriminative and quantitative models were then constructed using the 12 wavelengths. The discriminative model achieved a 100% identification rate for HA from different sources. The correlation coefficient of calibration (Rc), validation (Rp), external test (Rt), root mean square error of cross validation (RMSECV), calibration (RMSEC), validation (RMSEP), and external test (RMSET) of the mixed proportion quantitative model were 0.9876, 0.9876, 0.9898, 0.0546, 0.0433, 0.0440, and 0.0347, respectively. In this study, the problem of structural similarity and non-identifiability of HA produced by acidolysis and enzymatic hydrolysis was addressed, and quality monitoring of HA feedstock in HA circulating links was achieved. This is the first time to achieve accurate quantification of solid mixtures using the aquaphotomics method.