Heteroatom-doped graphene serves as a metal-free cathode catalyst in fuel cells, and has attracted great attention because of its low-cost, abundance, high activity, and robust stability. However, the heteroatom configuration in the graphene sheet is difficult to control, which prevents an understanding of the catalytic mechanisms and synthesis strategies. Herein, we introduce an organic condensation method to selectively functionalize graphene edges and defects with heterocycles under mild conditions. This method is an efficient way to dope graphene with structure-defined heteroatom clusters. By this method, the as-prepared heteroatom-doped graphene shows promising performance for oxygen reduction reaction in alkaline conditions with a preferred four-electron transfer process, demonstrating that graphene containing heteroatom clusters have high catalytic activity as metal-free cathodes.