Abstract: Agriculture is the cornerstone of economic development in China to serve a solid foundation for food security over the last three decades. However, the rapid increases in crop and animal production have caused serious non-point pollution, while farmers have received limited benefits, where the countryside and natural habitats have been insufficiently protected. Since great contributions have been made to mitigate the pollution over past decades, the pollution induced by agriculture are still great challenge. Since 2018, the rural revitalization led by the construction of ecological civilization marks the beginning of a new era in the treatment of agricultural non-point source pollution with higher requirements. In this study, an attempt was made on the shortage, and challenges of agricultural non-point source pollution control in modern agriculture. Currently, a systematical investigation is still lacking, particularly on the occurrence mechanism of environmental pollutants at the interface, microorganism and molecular scale. In the phase of pollutant migration, transformation and absorption, there is a lack of accurate traceability technology. In the aspect of model simulation, the parametrization of non-point source pollution mechanism, rationalization of model parameters and modularization of management measures need to be strengthened. In terms of technology, the traditional mode of relying on single source governance that "fixes the point and the line but not the watershed" cannot achieve the effect of overall optimization. This study focused on the major existing challenges of agro-ecological environment in China, further to propose that ecological cycle of agricultural industries practicing with a watershed orientation. The watershed management can be the core of agricultural non-point source pollution control. The traditional linear production mode of "resources-product-waste discharge" in the main grain production areas can be transformed into the combination of multi-dimensional and multi-levels of watershed, recycling, and benefit-oriented. Excessive nitrogen and phosphorus from manure can contribute to substantial damage and costs to the environment and human health. Meanwhile, animal manure is the major source of additional nutrients and crucial for maintaining soil organic matter and crop yield in traditional farming systems. The integration of cropping and livestock with cycling industrial chain can be considered as a key technology to control agricultural non-point source pollution. A better understanding the non-point pollution is necessary to take the lead in modern agricultural operations. Substantial promotion of agricultural non-point source pollution control depends mainly on a multi-dimensional governance participation, a sound system of laws, regulations and policies, strong regulatory system, scientific and technological system, and effective performance evaluation system. The involvement of farmers and agricultural entrepreneurs in pollution control action is a systematic maintenance to ensure the full control of agricultural non-point source pollution. Two ways can be: 1) Working directly with transferring knowledge to farmers through organized farmer cooperatives; and 2) enterprise-based approaches embodying relevant scientific results into commercial products. The theory has been testified with the typical example of agricultural non-point source pollution control in Qintaihe watershed of Binzhou, Shandong Province. An ecological recycling industrial chain of cropping and breeding has been built in Binzhou. A recycling path of waste recycling was explored with "double wheel drive" of government enterprises and "escort" of scientific research institutions. Local leading enterprises have played an important role with the advantages of industrial techniques for non-point source pollution control, integrating the recycling of agricultural organic waste into the clean planting of high-quality wheat planting and ecological pig breeding, and further to bridge the gap of agricultural pollution control and development of agricultural modernization industry. The finding can provide a valuable guidance for the construction of ecological and environmental system for the agricultural practices in the new era of China.