<p>Fossils preserve crucial information about the underlying biological and ecological processes of past ecosystems. Models built on paleontological and paleoecological data can help to elucidate the factors influencing ecosystem health, stability, resilience and function, offering a unique perspective on the long-term ecological impacts of the ongoing human-induced biodiversity crisis and ecosystem degradation. Substantial advances have been made in quantifying the ecological dynamics and functional structures of paleocommunities. However, the effective reconstruction of paleo-food webs and the quantitative evaluation of paleocommunity dynamics are still challenging tasks. Here we present a detailed protocol for reconstructing paleo-food webs using fossil data and for modeling the stability and structures of these paleocommunities using the cascading extinction on graphs model. The procedure includes (1) selecting an appropriate geological time range and geographic scope, collecting fossil data and reconstructing paleocommunities; (2) assigning species to guilds on the basis of shared prey–predator relationships and connecting the guilds that interacted trophically; (3) measuring the functional structures and modeling their dynamics using species-level networks and cascading extinction on graphs models; and (4) analyzing the results to understand the community evolution and identify tipping points that predict ecosystem collapse. Organismal expertise is needed in the reconstruction of paleo-food webs. The resulting comparisons of the paleocommunity stability and structure can help calibrate the timing and patterns of ecological changes during critical intervals in Earth history. This Protocol aims to enhance the utilization of ecological modeling in understanding the evolution of ancient ecosystems. The time required for the protocol is community size dependent — for example, ~5 months for communities containing ~1,000 species.</p>