Carbon nanomaterials such as graphene, carbon nanotubes, and fullerene have drawn great interest during the last decade due to their unique electrical, mechanical, thermal, and optical properties. By further combining these carbon nanomaterials with external nanocrystals of metal, semiconductor, ceramic, and/or quantum dot, it is possible to achieve the evolution of nanoscale hybrids and heterostructures with mutually improved performances and multi-functionalities. In this critical review, we summarize the state-of-the-art of recent researches on the development of nanoscale hybrids and heterostructures by incorporating carbon nanomaterials with foreign nanocrystals. The discussion is also focused on nanocomposites ranging from zero-dimensional to three-dimensional according to their fabrication approaches, structural properties, and applications. With respect to the practical applications of such nano-carbon-based hybrids and heterostructures, further review was presented on the recent development of carbon-tin based nanocomposites as electrode materials for lithium-ion batteries. The behaviors of carbon materials and their interaction with tin components during the charging/discharging of such lithium-ion batteries are summarized in detail. This review article is to provide critical knowledge and inspiration for future development of nano-carbon-based hybrids and heterostructures and their application in energy conversion and storage devices.