The development of efficient detection technology for dairy allergens represents a crucial concern for public health. In this study, a strategy utilizing sinapinic acid salt (SAS) for analyzing allergen proteins through MALDI-TOF MS is presented. SAS has proven to be a superior matrix compared to solid matrices, as it inhibits aggregation and prevents fragmentation, thereby yielding more reliable molecular mass values of intact allergen proteins. Furthermore, our results indicate that SAS offers higher sensitivity than solid matrices for milk protein analysis. The use of SAS also results in excellent repeatability and a strong linear relationship. By directly analyzing commercially available dairy products, this method has been confirmed to accurately differentiate allergen proteins across various types and brands of dairy products, and it is promising as a novel tool for detecting dairy allergen proteins in the future.