Abstract: Agriculture supports humankind’s sustainable existence on earth, exhibiting a complete spectrum of production, livelihood, ecology, and life characteristics. The prevailing model of modern conventional agriculture has made astonishing achievements in economic productivity but at the cost of ecological productivity because it was measured uniquely by market analysis under the ideology of neoclassical economics and equipped with manufactured materials from modern science and technology. Therefore, it is imperative to transform modern conventional agriculture into modern ecological agriculture, as instructed by agroecological principles and systematic science methodology, and the latter will be a vital pathway for state-specific agricultural modernization in China. For the sound development of Chinese ecological agriculture (CEA), the authors addressed three main missions, including transforming the agricultural industry from focusing on pure economic return to supporting public life, converting agricultural production from an ecologically vicious circle to an ecologically virtuous circle, and promoting agricultural administration from a broken chain to “cropping-husbandry-processing” and “agriculture-industry-service” integrations. The three technology categories include a multi-dimensional land use system for fully and efficiently utilizing the spatio-temporal resources, a material and energy recycling system for building a self-clean production, and an integrated pest management system for securing land and food. The three policy mechanisms include updating the theoretical system of CEA by promoting the agroecology discipline, fully realizing the eco-product value of ecological agriculture through the sound agroecological compensation institution, and ensuring the effective governance of territorial resources via unifying the spatial planning.