Mesoporous hollow carbon nanospheres (MHCS) have been extensively studied owning to their unique structural features and diverse potential applications. A surfactant‐free self‐assembly approach between resorcinol/formaldehyde and silicon alkoxide has emerged as an important strategy to prepare MHCS. Extending such a strategy to other substituted phenols to produce heterogeneous‐atom‐doped MHCS remains a challenge due to the very different polymerization kinetics of various resins. Herein, we report an ethylenediamine‐assisted strategy to control the cooperative self‐assembly between a 3‐aminophenol/formaldehyde resin and silica templates. Nitrogen‐doped mesoporous invaginated carbon nanospheres (N‐MICS) with an N content of 6.18 at %, high specific surface areas (up to 1118 m2 g−1), large pore volumes (2.47 cm3 g−1), and tunable mesopores (3.7–11.1 nm) have been prepared. When used as electrical double‐layer supercapacitors, N‐MICS show a high capacitance of 261 F g−1, an outstanding cycling stability (≈94 % capacitance retention after 10 000 cycles), and a good rate performance.