Fabrication of metal-organic frameworks (MOFs) or carbon-based materials with unique morphologies, such as one-dimensional (1D) nanofibers, is critical for energy storage and conversion applications because of their high surface area and efficient electron transport. This study presents a thermodynamically driven reconstruction strategy for the synthesis of sea-urchin-like MOF superstructures. Through this method, MOF block crystals are transformed into a pure-phase, sea-urchin-like superstructure comprising long, ultrathin, uniform MOF nanofibers. This evolution process involves reorganization of the coordination mode between ligands and metal centers, leading to reconstruction of the crystal structure. Detailed investigation into the evolution process demonstrate that the addition of urea can substantially expedite the reconstruction process. The free energy difference serves as the driving force of evolution from the initial kinetic intermediate state to the final thermodynamically stable state. Owing to the special nanofiber morphology, the derived Co- and N-codoped carbon nanofibers (Co-N-CNFs) offer exceptional advantages in boosting the oxygen reduction reaction (ORR) performance and are considerably superior to block-like CoNC electrocatalysts in terms of half-wave potential, stability, and durability. Zn-air battery test results confirm the remarkable ORR performance in practical applications, demonstrating the application potential of this new electrocatalyst for ORR. The proposed MOF reconstruction strategy offers a new pathway for synthesizing functional MOFs or their derivatives with 1D or other types of morphologies.