The copper-cobalt metal oxide composite magnesium oxide catalyst loaded with Ru has achieved the aerobic oxidation of 5-hydroxymethylfurfural (HMF) to the bio-based polyester monomer 2,5-furandicarboxylic acid (FDCA) under base-free conditions. Several Ru/Cu-Co-O·MgO catalysts were prepared, with Cu-Co-O being a combination of CuO and Co3O4. The catalyst's activity was boosted by the synergistic interaction between copper and cobalt, as well as an optimal copper-to-cobalt molar ratio. Optimal catalytic activity was observed in the Ru4/Cu1-Co1-O·MgO catalyst, loaded with 4 wt% Ru when copper-to-cobalt molar ratio of 1:1 and magnesium oxide compounding amount of 6 mmol were employed. The inclusion of MgO and the load of Ru not only expanded the specific surface area of the catalyst but also heightened its basicity. Additionally, the presence of loaded Ru improved the catalyst's reducibility at low temperatures. In aqueous solution under oxygen pressure, the conversion rate of HMF achieved 100%, and the yield of FDCA was 86.1%. After five reaction cycles, examining the catalyst and solution revealed that Ru nanoparticles resisted leaching or oxidation, and MgO exhibited only slight dissolution. The green separation of the product was achieved using semi-preparative liquid chromatography, selectively collecting the FDCA-containing solution by exploiting variations in interactions between solutes and the stationary/mobile phases. The subsequent steps involved rotary evaporation and drying, resulting in FDCA powder with a purity exceeding 99%. Notably, this approach eliminated the need to introduce concentrated hydrochloric acid into the system for FDCA separation, providing a novel method for synthesising powdered FDCA.