Lactic acid bacteria lyophilized preparations are widely used in the food, feed, and pharmaceutical industries; however, multiple stresses during the freeze-drying process often lead to a significant decline in bacterial viability. Improving their survival rate during lyophilization and storage stability remains a key industrial demand and research focus. This article reviews the mechanisms of freeze-drying damage in lactic acid bacteria, including mechanical injury from ice crystals, disruption of membrane phospholipids and alteration of fatty acid composition, osmotic imbalance, denaturation of proteins and key enzymes, and structural damage to genetic material. Strategies to improve the survival rate of lactic acid bacteria during freeze-drying were summarized, covering aspects such as medium composition, culture conditions, multiple stress pretreatments, protectant formulations, and control of centrifugation conditions and protectant mixing ratios. The influence of process parameters such as pre-freezing cooling rate, drying temperature and vacuum degree, as well as alginate-chitosan and lipid-based materials, storage temperature and humidity, and light exposure on the storage stability was analyzed. Finally, the current challenges in the analysis of damage mechanisms, process scaling, and industrial production were summarized, and the application prospects in high-activity and storage-resistant probiotic products were also envisioned. This is in the hope of providing theoretical references for the design and industrial production of freeze-dried lactic acid bacteria products.