In recent years, the sustainable management of agricultural and ecological systems has become a major challenge. Sustainable management has to solve crucial environmental problems linked, in part, to rapid changes in context: climatic changes, agricultural policy objectives changes, and so on. Solving this challenge involves the joint development of research in modelling, simulation, and virtual experimentation. In this chapter, we present some recent work devoted to the modelling and simulation of complex systems involved in agroecosystem management. Then, we present new formalisms for management strategies design, based on the weighted constraint satisfaction problems or the Markov decision processes frameworks. We also show how simulation and conception of strategies can be integrated. Finally, we illustrate the use of the presented approaches on several case studies in agroecosystems management, jointly tackled with research teams in agronomy.