Agricultural whole chain standardization (AWCS) is crucial for ensuring the security and stability of the agricultural industry of China and for promoting the transformation and upgrading of the industry. Currently, AWCS in China is faced with major challenges, including continuous optimization of the standards supply structure, urgent need to enhance the coordination between standards for different links, and prominent linkage barriers. This study analyzes the realistic values of the transformation of AWCS from the aspects of stability and security of the supply chain, smooth flow of elements of all links, innovation of production and operation modes, improvement in brand competitiveness, and low-carbon transformation. Additionally, the study proposes that the transformation of AWCS should focus on the following aspects: (1) comprehensive and complex problems of the industry; (2) coordination of pre-production, production, and post-production standards; (3) effective supply of high-quality standards; and (4) participation of all stakeholders. To the end, it is necessary to improve the effective supply of high-quality standards, promote the coordinated governance of standards across the entire industry chain, establish a connectivity mechanism for local standards, and strengthen the innovation of standards implementation mechanisms.