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Description: Fossil encodes essential information on many underlying biological and ecological processes. Modellings based on palaeontology and palaeoecological data have the potential to inform us the underlying processes contributing to ecosystem health, stability, resilience, and functioning. This historical perspective offers a unique lens through which we can understand the nature and potential long-term ecological impacts of the ongoing human-induced biodiversity crisis. Quantification of ecological dynamics and functional structures of palaeocommunities has seen substantial advances in recent years. However, effectively reconstructing palaeo-food web and evaluating palaeocommunity dynamics remain challenging. Here we present a protocol explains how to reconstruct palaeo-communities and palaeo-food webs using fossil data. The major stages include: (i) selecting an appropriate geological time range and geographic scope, collecting fossil data, and reconstructing palaeo-communities; (ii) assigning species to guilds if they share the same potential prey and predators, and connecting the guilds that possibly interact together; (iii) measuring functional structure of palaeo-communities and modeling their dynamics by using species-level network and cascading extinction on graphs models; and based on the above results, (iv) drawing insights from the results obtained to analyze the process of community evolution and identifying the key ecosystem tipping points. It enables a quantitative comparation of stability and structure of palaeo-communities that can be used to calibrate the timing and pattern of ecological change during critical time intervals in Earth history. We anticipate that this protocol will help the geobiologists make the best use of this modeling tool for studying the evolution of ancient ecosystems.