A two-layer DSS for rural sustainable development (DRSD) was developed for the comprehensive planning of socioeconomic development and eco-environment protection in Yongxin County, Jiangxi Province, China. The DRSD considers multiple sectors within a general decision-support framework to generate cross-sector optimal development schemes at a county scale. It integrates a dynamic database system, large-scale linear programming for regional managers, and integer linear programming for farmers, which makes a solid step toward linking farmers' microplanning with administrators' macropolicies. Yongxin, an economically relatively undeveloped and geographically relatively isolated county, was chosen as the paradigm for this DRSD application; this selection provided a good opportunity to analyze the relationships between rapid economic development, ecological destruction, and environmental deterioration within the region. The results from the representative scenario, Sustainable Development, suggested that maximization of overall economic benefits for 23 towns in Yongxin over a 15-year period, from 2007 to 2022 would require relatively small increases in agricultural and horticultural areas, significant increases in scales of livestock, poultry, sericulture, forestry, and fisheries, as well as significant increases in investment in both the secondary and the tertiary industry sectors. Future directions and implementation challenges for this type of DSS were discussed.