Abstract: China boasts a long history of agricultural civilization, with traditions and experiences accumulated over time in utilizing natural resources to enrich soil and increase crop yields, placing China’s crop production technology at the forefront of the world for an extended period. The emergence and development of the modern fertilizer industry have significantly diminished the role of natural organic resources in China’s grain production. Even today, when green development is emphasized, due to factors such as application costs and application habits, the use of organic fertilizers in food crops remains far less than that in economic crops. Wheat is a staple food crop in China, and over-reliance on chemical fertilizers not only affects the soil productivity of wheat fields but also constrains the improvement of wheat quality, yield, efficiency, and green sustainable production. There is an urgent need to re-recognize the role of organic fertilizers from both theoretical and practical perspectives. This paper reviews the history and current status of organic fertilizer application in China and summarizes the effects of organic fertilizer application on improving soil properties, wheat yield, quality, and nutrient use efficiency in wheat fields. Currently, there are 433 types of traditional organic fertilizers in 10 categories in China, with three additional categories of commercial organic fertilizers having been added in recent years. Numerous studies have demonstrated that organic fertilizer application can improve soil structure and organic matter stability to varying degrees, enhance soil water retention and stable nutrient supply capacity, maintain the stoichiometric balance between soil nutrients and microorganisms, buffer nematode stress caused by excessive nitrogen fertilizer, sustain soil food web functions, and mitigate the impact of climate change on soil micro-ecological environments. The multifaceted functions of organic fertilizers in soil explain their mechanism for increasing wheat yield, nutritional and processing quality. Research on organic fertilizer application techniques has also made meaningful progress, proving that in most regions of China, neither sole nor heavy application of organic fertilizers can meet current food security needs. Only through rational combined application with chemical fertilizers can the roles of both be fully leveraged to achieve simultaneous improvements in wheat yield, quality, and soil fertility. Many regions have proposed substitution equivalents for chemical nitrogen and phosphorus nutrients with different organic fertilizers, and have used big data to propose ranges of proportions for replacing chemical fertilizers with organic fertilizers tailored to different goals. Years of research data and multi-source integration with artificial intelligence provide a platform for precise and specialized utilization of compost. However, besides innovations in application rates, methods, and machinery for organic fertilizer application, new problems have arisen from organic waste (sources of organic fertilizer) in modern agriculture, such as the enrichment of heavy metals in livestock and poultry manure and the introduction of antibiotics, microplastics, antibiotic resistance genes, and persistent organic pollutants into soil through the application of organic fertilizers. Therefore, the scientific and rational application of organic fertilizers requires concerted efforts from governments, enterprises, research institutions, grassroots extension personnel, and farmers. Guided by national strategic needs and driven by farmers’ demands, targeted research should be conducted starting from production practice issues to solve key problems, innovate and develop new organic fertilizer products and technologies, and formulate targeted policy documents. These efforts will ensure the scientific promotion and application of organic fertilizers in China and achieve green and sustainable agricultural development.