The paper classifies all the groups of paths as first passage paths (set φ) and subsequent passage paths (set ρ), and explains the calculation method of the throughflow under the models φ and ρ by the input-output flow analysis. We chose the five-compartment model of ecological network proposed by Pilette and Kincaid as an example, and calculate TST_φ and TST_Ω, then quantitatively derive a correct evaluation influences of φ and ρ on ecological network throughflow. The results show that: the total system throughflow is 31g C every day, and 90.23 percent of the total system throughflow corresponds to the model φ, 9.77 percent of the total system throughflow related to the model ρ. Finally, we respectively analyze how the models φ and ρ influence the throughflow of every node in the ecological network. The non-measurable, unobservable and indirect properties developed by input-output analysis can provide a deeper insight into the ecosystem, thus offering quantitative methods for exploring indirect effects and interconnectivity.