The invention provides an index system modeling system of petrochemical environmental protection management and a modeling method thereof. From three levels of an environmental protection index of petrochemical-enterprise environmental protection management, an accounting unit and an accounting attribute, an index system model is constructed. Enterprise environmental protection management information is guaranteed to be established on a model with a uniform standard, and an actual demand of enterprise environmental protection management whose transverse direction is to an edge and longitudinal direction is to a bottom is satisfied. A foundation is laid for standard performance of enterprise environmental protection statistics informatization and environmental protection data accounting caliber consistency so that enterprise environmental protection management and a scientific decision are effectively supported.