Paddy rice-upland crop rotation system is a major cropping system in China, and practiced widely along the Yangtze River basin. A unique feature of this system is the annual conversion of soil from aerobic to anaerobic and then back to aerobic condition, which can result in the changes of soil physical, chemical, and biological prosperities among seasons, making a special agroecosystem. The major challenges faced by this system include declining or stagnating productivity, increasing shortage of irrigation water, improper management of nutrients, low efficiency of resource utilization, and environmental pollution. Based on an overview of the characteristics and problems of paddy rice-upland crop rotation system, this paper put forward a strategy of practicing integrated nutrient management to solve the contradictions between nutrient input, crop production and environmental risk. The key points of this strategy included nutrient management from the whole rotation system perspective, integrated use of nutrients from various sources (chemical fertilizers, organic fertilizers, and nutrients from the environment), synchronization of nutrient supply and crop nutrient demand, application of different management technologies based on the characteristics of different nutrient resources, and integration of nutrient management with other cropping system technologies like water saving and high-yielding cultivation, etc.