Metal-free carbon, as the most representative heterogeneous metal-free catalysts, have received considerable interests in electro- and thermo-catalytic reactions due to their impressive performance and sustainability. Over the past decade, well-designed carbon catalysts with tunable structures and heteroatom groups coupled with various characterization techniques have proposed numerous reaction mechanisms. However, active sites, key intermediate species, precise structure–activity relationships and dynamic evolution processes of carbon catalysts are still rife with controversies due to the monotony and limitation of used experimental methods. In this Review, we summarize the extensive efforts on model catalysts since the 2000s, particularly in the past decade, to overcome the influences of material and structure limitations in metal-free carbon catalysis. Using both nanomolecule model and bulk model, the real contribution of each alien species, defect and edge configuration to a series of fundamentally important reactions, such as thermocatalytic reactions, electrocatalytic reactions, were systematically studied. Combined with in situ techniques, isotope labeling and size control, the detailed reaction mechanisms, the precise 2D structure–activity relationships and the rate-determining steps were revealed at a molecular level. Furthermore, the outlook of model carbon catalysis has also been proposed in this work.