Milk serum contains many immune-active proteins that are sensitive to heat treatment. This study compared the effects of thermal (63 °C, 30 min; 72 °C, 15 s; 85 °C, 5 min) and non-thermal (ultraviolet-C, UV-C; thermo-ultrasonication, TUS) treatments on bovine milk serum proteins by using label-free LC-MS/MS-based proteomics. UV-C (4500 J/L) and TUS (60 W, 6 min) treatments achieved a 5log microbial reduction as determined by plate counting. Proteomics showed that e.g., complement proteins, xanthine dehydrogenase/oxidase, and fatty acid-binding protein decreased significantly (p˂0.05, |fold change|˃1) after thermal treatments, and almost no lactoferrin, immunoglobulin, and lactoperoxidase was retained after heating at 85 °C for 5 min, whereas these proteins were mostly retained after non-thermal treatments. Most of these heat-sensitive proteins were located in membrane and extracellular regions and were involved in cellular and metabolic processes, response to stimulus, binding, immune process and catalytic functions. Finally, part of the proteomics results were verified by ELISA. This study thus provided insights for the development of optimized thermal and novel non-thermal treatments for dairy processing. Industrial relevance: As alternatives to thermal processing technique, UV-C and ultrasonication showed a great potential in the processing of milk. This study not only showed that UV-C and ultrasonication were able to largely reduce the microbial load of raw milk, but also better retained the immune-related milk serum proteins than thermal processing, especially for the UV-C treatment. ELISA assays also demonstrated that the LC-MS/MS based proteomics technology used in this study was a robust method for quantifying damage to the milk serum proteome upon processing. Taken together, this study provided insights for development of optimized thermal and novel non-thermal techniques for dairy processing.