Yolk-shell carbon nanospheres (YSCNs) have raised a great deal of interest due to the synergistic advantages over their counterparts. However, it is still difficult to precisely regulate the morphology, porosity, and composition of YSCNs. Here, N-doped porous YSCNs were synthesized via an in situ self-activation by pyrolysis of polypyrrole encapsulated hyper-cross-linked polystyrene (HPS@PPy) core-shell nanospheres, followed by a mild air activation treatment. During the self-activation process, the polypyrrole shell of HPS@PPy provided a confinement effect for the morphology transformation from the core-shell to the yolk-shell structure. The air activation exhibited simultaneous control over porosity and composition. The preparation parameters, such as shell thickness and air activation conditions, were modified to optimize the structure and surface composition of YSCNs to achieve optimal electrochemical performances.