The Fenton reaction is recognized as an effective technique for degrading persistent organic pollutants, such as the emerging pollutant trimethoprim (TMP). Recently, due to the excellent reducibility of active hydrogen ([H]), Pd–H2 has been preferred for Fenton-like reactions and the specific H2 activation of Pd-based catalysts. Herein, a heterogeneous Fenton catalyst named the hydrogen-accelerated oxygen reduction Fenton (MHORF@UiO-66(Zr)) system was prepared through the strategy of building ships in the bottle. The [H] has been used for the acceleration of the reduction of Fe(III) and self-generate H2O2. The systematic characterization demonstrated that the nano Pd0 particle was highly dispersed into the UiO-66(Zr). The results found that 20 mg L−1 of TMP was thoroughly degraded within 90 min in the MHORF@UiO-66(Zr) system under conditions of initial pH 3, 30 mL min−1 H2, 2 g L−1 Pd@UiO-66(Zr) and 25 μM Fe2+. The hydroxyl radical as well as the singlet oxygen were evidenced to be the main reactive oxygen species by scavenging experiments and electron spin resonance. In addition, both reducing Fe(III) and self-generating H2O2 could be achieved due to the strong metal-support interaction (SMSI) between the nano Pd0 particles and UiO-66(Zr) confirmed by the correlation results of XPS and calculation of density functional theory. Finally, the working mechanism of the MHORF@UiO-66(Zr) system and the possible degradation pathway of the TMP have been proposed. The novel system exhibited excellent reusability and stability after six cyclic reaction processes.