From the orientation of the global baked food industry toward health and sustainable development in recent years, this paper systematically reviews the innovations and progress across three core dimensions: raw material substitution, process optimization, and packaging improvement. First, regarding raw materials, conventional wheat flour is replaced with ingredients such as whole-grain flours and plant-based food by-products. Natural functional additives and novel protein sources (e.g., plant proteins, insect proteins, and microbial proteins) are developed to enhance the nutritional and health value of products and realize the efficient utilization of resources. Second, in the core process, techniques such as dough mixing, fermentation, and baking are optimized to retain more nutritional components. Meanwhile, low-carbon processes including waste heat recovery and flexible production are pioneered to reduce processing energy consumption and carbon emissions. Finally, at the packaging stage, new materials such as natural polymer composite films and functional paper, along with intelligent preservation technologies, are adopted to establish a packaging system characterized by reduction and circular development.