Ecological systems can have alternative stable states (ASS) that potentially lead to the drastic change of the state of a system(called regime shift) when an external perturbation pushes the system out of the basin of attraction of one state to a different state. In this situation, recoverability to the original state owes to the structure of the basin of attraction, and this type of “stability” is defined as “ecological resilience” by Holling (1996). The structure of the basin boundary is essential for the understanding of ecological resilience. However,it is not easily obtained if the number of interacting species is large and especially if the system exhibits non-equilibrium population dynamics such as population cycles, which has limitedthe quantification of ecological resilience so far. In this study, we propose a numerical method that we can easily obtain the information of the basin boundary even if the system contains many species and exhibits non-equilibrium dynamics. Here, we show how the ecological resilience fluctuates time to time and differs depending on the trophic position of a species of interest, using a three-species model as an example. Our results suggest that ecological resilience can be incorrectly estimated if the structure of basin boundaries is analyzed in a simple abstracted model showing only equilibrium dynamics.