Mass extinctions are considered to be quintessential examples of Court Jester drivers of macroevolution, whereby abiotic pressures drive a suite of extinctions leading to huge ecosystem changes across geological timescales. Most research on mass extinctions ignores species interactions and community structure, limiting inference about which and why species go extinct, and how Red Queen processes that link speciation to extinction rates affect the subsequent recovery of biodiversity, structure and function. Here, we apply network reconstruction, secondary extinction modelling and community structure analysis to the Early Toarcian (Lower Jurassic; 183 Ma) Extinction Event and recovery. We find that primary extinctions targeted towards infaunal guilds, which caused secondary extinction cascades to higher trophic levels, reproduce the empirical post-extinction community most accurately. We find that the extinction event caused a switch from a diverse community with high levels of functional redundancy to a less diverse, more densely connected community of generalists. Recovery was characterised by a return to pre-extinction levels of some elements of community structure and function prior to the recovery of biodiversity. Full ecosystem recovery took ~7 million years at which point we see evidence of dramatically increased vertical structure linked to the Mesozoic Marine Revolution and modern marine ecosystem structure.