The invention relates to a preparation method for a fatty acid starch ester and application thereof, which belongs to the technical field of modified starch. According to the invention, starch is adopted as a raw material and fatty acid is taken as an esterification agent; and on the condition of taking an extruder as a chemical reactor, the acidolysis and esterification modification of the starch is carried out to prepare the fatty acid starch ester product with the low substitution degree. The fatty acid which is subjected to the high temperature high pressure high shearing action treatment of the extruder has an esterification reaction with crude starch according to a certain proportion; and due to the introduction of the hydrophobic organic carbon chain, the starch has the lipophilicity and hydrophilicity, and consequently has certain emulsibility. The product can be used as a stabilizer, an emulsifier, a gelling agent, a fat substitute, a microcapsule wall material, and the like in the food industry, and can be applied to the foods such as artificial butter, salad seasoning matter, bakery products, diary products, and the like. The invention has the advantages that the extruder is adopted to prepare the esterified starch; the reaction process is continuous and has simple operation, easy implementation and little environmental pollution; and the obtained product has excellent performance.