Abstract: An evaluation system of comprehensive benefits of eco-agriculture has been established using the theorem of system engineering combined with statistics and analytical hierarchy process. Comprehensive benefits of eco-agriculture are divided into three sub-benefits, which are economic benefit, ecological and environmental benefit and social benefit. Every sub-benefit is divided into several indexes, which can be quantified directly.Weight coefficient reflects the contributing degrees of the indexes. Values of sub-benefits and compreh ensive benefits are obtained through adding up all of the weight values of sub-benefits.