The whole industrial chain standards system of modern agriculture is a new standards system that is guided by market demand and integrates all production factors and the entire production process of agriculture; it is developed against the background of agricultural supply-side reforms in China and has become a cornerstone for the rural revitalization strategy and the high-quality development of China’s agriculture. In this article, we first summarize the demand for the whole industrial chain standards system and analyze the opportunities and challenges faced by China in the construction of this standards system. Subsequently, we explore the connotation and guidelines of the standards system and propose a three-tier framework for this system. Furthermore, a development path and countermeasures are proposed. Specifically, the construction of the whole industrial chain standards system should focus on five aspects: formulation and revision of key standards, cultivation of standardization personnel, innovation of the agricultural standardization service mode, internationalization of industry standards, and establishment of industry associations’standards. Moreover, to construct the whole industrial chain standards system, China should establish a coordinated working mechanism, strengthen demonstrations, conduct effect evaluation of the standardization, and improve its supervision system.