Structural engineering is an effective methodology for the tailoring of the quantities of active sites in nanostructured materials for fuel cell applications. In the present study, Co nanoparticles were incorporated into the network of 3D nitrogen-doped carbon tubes (Co@NCNTs) that were obtained via the molten-salt synthetic approach at 800 °C. Morphological representation reveals that the Co@NCNTs are encompassed with Co nanoparticles on the surface of the mesoporous walls of the carbon nanotubes, which offers a significant active surface area for electrochemical reactions. The CoNPs/NCNTs-1 (treated with CaCl2) nanomaterial was used as a potential candidate for the electro-oxidation of hydrazine, which improved the response of hydrazine (~8.5 mA) in 1.0 M NaOH, as compared with CoNPs/NCNTs-2 (treated without CaCl2), NCNTs, and the unmodified GCE. Furthermore, the integration of Co helps to improve the conductivity and promote the lower onset electro-oxidation potential (−0.58 V) toward the hydrazine electro-oxidation reaction. In particular, the CoNPs/NCNTs-1 catalysts showed significant catalytic activity and stability performances i.e., the i-t curves showed notable stability when compared with their initial current responses, even after 10 days, which indicates the significant durability of the catalyst materials. This work could present a new approach for the design of efficient electrode materials, which can be used as a favorable candidate for the electro-oxidation of liquid fuels in fuel cell applications.