N-hydroxyphthalimide (NHPI) is a powerful green nitrogen-containing free radical catalyst, while the leaching of homogeneous NHPI remains a crucial obstacle. Herein, the cobalt-based metal–organic frameworks (Co-based MOFs) were introduced as the supports and co-catalysts to successfully confine the NHPI catalyst. NH3-TPD characterization confirmed that the heterogeneous catalyst NHPI@Co-MOF containing carboxyl groups linker exhibits more assertive acidity, facilitating the activation of O2 to generate active radicals O2•− that determined the catalytic activity. Owing to these features, NHPI@Co-MOF-DA with two carboxyl groups as the linker achieved 98 % of DBT conversion at 120 °C. Moreover, the DBT conversion of the used catalyst reached 95 % after being recycled 10 times. The distinctive design strategy provided valuable insights into the selection of suitable organic linkers to enhance the synergistic effect of metal cobalt with NHPI in the oxidative desulfurization (ODS) process, broadening the research horizon of MOF hybrids in the construction of efficient ODS applications.