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Sustainable development and growth of agriculture sector calls for improving its competitiveness through a better understanding of lands, weather and climate, and planting, especially prediction of events with increased accuracy, and systematic integration of observations and prediction into decision-making in agriculture management. In this short paper, a systematic approach based on integrated information systems (IISs) for agricultural ecosystem management is proposed. The approach involves establishing an IIS called agricultural ecosystem enterprise information system (AEEIS) that extracts data on terrain, land use, planting, and others, and integrates them for the purpose of agricultural and ecosystem management. The integration helps in generating managerial/policy alternatives in consultation not only with agricultural and ecological specialists, but also with agriculture and ecosystems management. AEEIS, a platform of enterprise information systems, includes operational database, extract transform and load, data warehouse, data mining, simulation modeling, and knowledge management for generating managerial strategies on land use, planting species/variety, and optimal coverage of plants. AEEIS is part of efforts on integrated agricultural information services that is one of the main applications of China's sustainable agricultural development plan. The short paper concludes that, for effective management of agriculture and ecosystems, a systematic approach is essential in which IISs play a crucial role.