The addition of phosphotungstic acid (PTA) to the synthesis mixture of PdCu@Fe^III–MOF-5 yields the direct encapsulation of PTA inside the MOF structure (i.e. PTA@PdCu@Fe^III–MOF-5) through a facile solvothermal approach. The deoxygenation reaction of palmitic acid has been investigated over PdCu@Fe^III–MOF-5 and PTA@PdCu@Fe^III–MOF-5 under a hydrogen atmosphere in the supercritical fluid (SCF) of n-hexane. The results showed that palmitic acid can be converted completely at 240 °C on PTA@PdCu@Fe^III–MOF-5 with a high selectivity of hexadecane. Owning to the improvement of acidity of the MOF catalyst by the encapsulation of PTA inside the hollow octahedral nanostructures of PdCu@Fe^III–MOF-5, the selectivity for hexadecane over the PTA@PdCu@Fe^III–MOF-5 catalyst is higher than that over PdCu@Fe^III–MOF-5. The excellent performance in the catalytic hydrodeoxygenation (HDO) of palmitic acid is associated with the synergistic effect between yolk–shell PTA@PdCu@Fe^III–MOF-5 nanostructures and SCF medium.