With the rapid growth of the global population and the increasing demand for healthier diets, improving the nutrient utilization efficiency of staple food crops has become a critical scientific and industrial challenge, prompting innovation in food processing technologies. This review introduces first the common nutritional challenges in the processing of staple food crops, followed by the comprehensive examination of research aiming to enhance the nutritional quality of staple food crop-based foods through innovative processing technologies, including microwave (MW), pulsed electric field (PEF), ultrasound, modern fermentation technology, and enzyme technology. Additionally, soybean processing is used as an example to underscore the importance of integrating innovative processing technologies for optimizing nutrient utilization in staple food crops. Although these innovative processing technologies have demonstrated a significant potential to improve nutrient utilization efficiency and enhance the overall nutritional profile of staple food crop-based food products, their current limitations must be acknowledged and addressed in future research. Fortunately, advancements in science and technology will facilitate progress in food processing, enabling both the improvement of existing techniques as well as the development of entirely novel methodologies. This work aims to enhance the understanding of food practitioners on the way processing technologies may optimize nutrient utilization, thereby fostering innovation in food processing research and synergistic multi-technological strategies, ultimately providing valuable references to address global food security challenges.