Distinct from conventional carbon nanostructures, such as fullerene, graphene, and carbon nanotubes, carbon nanodots (C-dots) exhibit unique properties such as strong fluorescence, high photostability, chemical inertness, low toxicity, and biocompatibility. Various synthesis routes for C-dots have been developed in the last few years, and now intense research efforts have been focused on improving their functionality. In this aspect, doping and surface functionalization are two major ways to control the chemical, optical, and electrical properties of C-dots. Doping introduces atomic impurities into C-dots to modulate their electronic structure, and surface functionalization modifies the C-dot surface with functional molecules or polymers. In this review, we summarize recent progress in doping and surface functionalization of C-dots for improving their functionality, and offer insight into controlling the properties of C-dots for a variety of applications ranging from biomedicine to optoelectronics to energy.