Development of multi-ligand metal–organic frameworks (MOFs) and derived heteroatom-doped composites as efficient non-noble metal-based catalysts is highly desirable. However, rational design of these materials with controllable composition and structure remains a challenge. In this study, novel hierarchical N-doped CuO/Cu composites were synthesized by assembling dual-ligand MOFs via a solvent-induced coordination modulation/low-temperature pyrolysis method. Different from a homogeneous system, our heterogeneous nucleation strategy provided more flexible and cost-effective MOF production and offered efficient direction/shape-controlled synthesis, resulting in a faster reaction and more complete conversion. After pyrolysis, they further transformed to a unique metal/carbon matrix with regular morphology and, as a hot template, guided the orderly generation of metal oxides, eliminating sintering and agglomeration of metal oxides and initiating a synergistic effect between the N-doped metal oxide/metal and carbon matrix. The prepared N-doped CuO/Cu catalysts held unique water resistance and superior catalytic activity (100% CO conversion at 140 °C).