The paper selected 20 benefit indicators relating to economy, society, and ecology. It used improved FAHP to build a comprehensive evaluation model for large hydro-junction project. Taking Jiangdu hydro-junction for example,it thought the comprehensive benefit situation of Jiangdu hydro-junction project under the scenarios of ecological environment and normal situation.The results show that Jiangdu hydro-junction has notable benefit,all of the level eigenvalues of economy, society and ecology environment benefits are above 4.2 The benefits in protecting port,improving green coverage,increasing local visibility and preventing natural disaster are espically outstanding.The eigenvalues of comprehensive benefit only only changes by 1.3% through disterbing perturbing layer weight distribution,which indicated that the weight distribution of rule layer has little effect on the assessment results of comprehensive efficiency.