Developing an efficient, hydrothermally stable and non-noble metal catalyst is a key for application of aqueous-phase reforming of methanol (APRM) to produce hydrogen in situ. Herein, a Cu@NC catalyst with high metal loading (44.9 wt %) and sub-6 nm Cu nanoparticle size was synthesized by pyrolyzing Cu-chitosan chelates. The coordination between metal ions (Cu2+) and amine functional groups in chitosan enabled high metallic dispersion in Cu-chitosan chelates. After pyrolysis, the Cu nanoparticles were embedded in N-doped carbon (NC) matrix. This confinement effect ensured remarkable hydrothermal stability for the Cu@NC catalyst. As a result, a high hydrogen production rate of 34.0 μmol·gcat−1·s−1 was obtained over Cu@NC-200 catalyst, about 12.6 times higher than that of a traditionally impregnated Cu/C catalyst. Notably, no deactivation and aggregation of Cu nanoparticle were observed after 200 h’ running in APRM, indicating excellent hydrothermal stability of the Cu@NC catalyst. Thus, this work developed a simple strategy to prepare an efficient and robust catalyst that could work well under hash hydrothermal conditions for application of APRM on the compact mobile devices.