At present, the catalytic conversion of carbon-containing resources remains a major challenge faced during the economic growth and energy mix adjustment around the world. The development of catalysts with high efficiency for the conversion of carbon-containing resources is one of the major solutions to the energy and environmental problems. During these conversion processes, carbon plays an essential role in the sense that it is not only the key element in the reactions but may also cause the modification of the chemical nature of the catalysts. Notably, comprehension of the structure−performance relationship of catalytic materials is the basis for catalyst development. In particular, the modulating role of carbon on the catalyst structures during the conversion of carbon-containing resources has attracted increasing attention. In the past five years, we have systematically studied the modulation of Fe-, Co-, Ni-, and Mo-based catalysts by carbon using theoretical approaches. In this review, with a focus on the active phases, morphologies, surface structures, electronic properties, and catalytic performances of transition-metal catalysts (Fe, Co, Ni, Mo, and other transition metals), the modulation of these catalysts by carbon will be summarized to shed light on the question of how to tune the behavior of carbon in terms of catalyst carburization and carbon-related surface reactions. This review provides systematic and fundamental information for the further design and development of catalysts for the conversion of carbon-containing resources.