Abstract: The agricultural ecosystem in South China plays an important role in the whole agricultural ecosystem in China. Southern agricultural ecosystem has some features, such as, complex structure, diverse function, high efficient production, precious value and huge development and utilization potential. At present, there is a series of problems in southern agriculture ecological system-arable land abandonment, soil fertility decline, soil pollution, frequent natural disasters, low efficiency and lack of stamina, which seriously restrict the sustainable development of southern agricultural ecological system. In order to achieve the sustainable development of agricultural ecosystem in South China, the following measures should be adopt:(1) implementation of intensive land use; (2) carrying out of environmental remediation; (3) implementation of fallow rotation; (4) combination of land use and protection; (5) optimization of agricultural ecosystem structure and (6) deepening of rural reform.