The rational design of carbon-supported transition-metal single-atom catalysts requires the precise arrangement of heteroatoms within the single-atom catalysts. However, achieving this design is challenging due to the collapse of the structure during the pyrolysis. Here, we introduce a topological heteroatom-transfer strategy to prevent the collapse and accurately control the P coordination in carbon-supported single-atom catalysts. As an illustration, we have prepared self-assembled helical fibers with encapsulated cavities. Within these cavities, adjustable functional groups can chelate metal ions (N x ···M n+ ···O y ), facilitating the preservation of the structure during the pyrolysis based phosphidation. This process allows for the transfer of heteroatoms from the assembly into single-atom catalysts, resulting in the precise coordination tailoring. Notably, the Co–P 2 N 2 –C catalyst exhibits electrocatalytic performance as a non-noble metal single-atom catalyst for alkaline hydrogen evolution, attaining a current density of 100 mA cm −2 with an overpotential of only 131 mV.