Freeze-drying technology has been widely applied in the storage of biomacromolecules. However, the stability of freeze-dried biomacromolecules poses significant challenges to the biotechnology industry, often leading to difficulties in development, storage, and transportation. Therefore, this study aims to investigate the molecular vibrational characteristics and thermal stability of freeze-dried biomacromolecules using THz-TDS, NIRS, and DSC. A comprehensive understanding of the behavior and properties of freeze-dried macromolecular materials is crucial for assessing their stability. This study selected four different types of milk (whole milk, skim milk, lactose-free whole milk, and lactose-free low-fat milk) as raw materials for freeze drying. A set of freeze-dried milk samples was stored for one week to examine moisture changes caused by hygroscopicity during storage. The results showed that lactose, lipids, and moisture in the samples could be effectively analyzed through the amplitude values and time shifts of terahertz time-domain spectroscopy, complex permittivity, near-infrared reflectance, and DSC thermal analysis curves. These findings provide valuable references for the stability analysis of freeze-dried biomacromolecules.