Human serum albumin (HSA) is the most abundant protein in plasma and plays an essential physiological role in the human body. Ethanol precipitation is the most widely used way to obtain HSA, and pH and ethanol are crucial factors affecting the process. In this study, infrared (IR) spectroscopy and near-infrared (NIR) spectroscopy in combination with chemometrics were used to investigate the changes in the secondary structure and hydration of HSA at acidic pH (5.6–3.2) and isoelectric pH when ethanol concentration was varied from 0% to 40% as a perturbation. IR spectroscopy combined with the two-dimensional correlation spectroscopy (2DCOS) analysis for acid pH system proved that the secondary structure of HSA changed significantly when pH was around 4.5. What’s more, the IR spectroscopy and 2DCOS analysis showed different secondary structure forms under different ethanol concentrations at the isoelectric pH. For the hydration effect analysis, NIR spectroscopy combined with the McCabe–Fisher method and aquaphotomics showed that the free hydrogen-bonded water fluctuates dynamically, with ethanol at 0–20% enhancing the hydrogen-bonded water clusters, while weak hydrogen-bonded water clusters were formed when the ethanol concentration increased continuously from 20% to 30%. These measurements provide new insights into the structural changes and changes in the hydration behavior of HSA, revealing the dynamic process of protein purification, and providing a theoretical basis for the selection of HSA alcoholic precipitation process parameters, as well as for further studies of complex biological systems.