Abstract: This paper sets the hierarchy of assessing fishery eco-environment advantage or disadvantage on the basis of the characteristics of Chaohu Lake fishery waters. With the results of biology survey and water quality monitoring, it sets compare matrixes between goal layer, index layers, vice-index layer and project layers by three-marking-degree law. Processed with mathematics, the judgment matrixes are built indirectly. The arrangement of classes to general aim is definite by the usual analytic hierarchy process finally. According to the fact of Chaohu Lake fishery waters, the advantage and/or disadvantage of fishery eco-environment is assessed.