Abstract Heat treatment is commonly used in wheat storage and processing. Proper heat treatments are beneficial to improve the storage stability, and processing, nutritional and eating quality of wheat and flour, which is of great significance for ensuring food safety and improving wheat quality. However, wheat quality may be influenced adversely by improper heat treatment. The heat treatment methods commonly used in wheat processing are summarized in this paper and their applications in killing of insect pests, sterilization, detoxification, enzymatic inactivation and quality improvement are reviewed. Meanwhile, the negative effects of heat treatment on wheat quality and some countermeasures are proposed. Therefore, it is necessary to comprehensively understand the changes in wheat and flour quality during heat treatment and to study the effects of heat treatment on the final product quality. Moreover, the mechanism underlying these changes should be explored in order to improve the heat treatment process in a targeted manner and to develop heat treatment equipment for industrial applications to reduce the cost of heat treatment. It is desired that this review will promote the continuous development of heat treatment technology for applications in wheat storage and processing.