Alpha-Amylase is a glycoside hydrolase that efficiently catalyzes the hydrolysis of starch and is widely applied in various industrial fields such as food, textile, and paper industries. It plays a pivotal role particularly in food processing processes such as starch liquefaction, baking improvement, and juice clarification. However, natural α-amylases generally exhibit poor thermal stability, weak acid tolerance, and strong calcium ion dependency, which severely restrict their application in complex industrial environments. In recent years, protein engineering technologies, including directed evolution, rational design, and semi-rational design, have been extensively employed to the structural optimization and performance improvement of α-amylases. This article systematically reviews the research progress of protein engineering in enhancing the thermal stability and acid tolerance of α-amylases, and summarizes their application outcomes in high-temperature starch liquefaction, anti-staling bread baking, and low-pH beverage clarification.