The embodiment of the invention discloses a method for detecting short-chain fatty acid in a milk product. The method comprises the following steps: (1) preparing a reference solution and a standard sample stock solution; (2) preparing a milk product solution; (3) performing GC-MS (gas chromatography-mass spectrometer) detection; (4) according to GC-MS detection results of the reference and milk product solutions, determining the type of short-chain fatty acid contained in the milk product; (5) calculating relative peak area of short-chain fatty acid. The method for detecting short-chain fatty acid in the milk product is simple, sensitive, quick, accurate, strong in specificity and good in repeatability, and can be used for quality control research on short-chain fatty acid in the milk product.