<p>Heterogeneous cobalt materials were important catalyst for the development of a more efficient cyclohexane oxidation process, however the catalytic performance of which should further be improved. Herein, hierarchical Silicalite-1 confined with cobalt as the active centers was hydrothermally synthesized, the chemical environment of Co and intracrystalline porosity were tuned, and the influences of which on cyclohexane oxidation was detailed studied. The cobalt in conventional Silicalite-1 was mainly four-coordinated. In the hierarchical catalyst prepared by silanization, intracrystalline mesopores in the 4.52–5.92&#xa0;nm range were created, and the mesopore volume ranged from 0.127 to 0.193 cm³/g. More importantly, although the cobalt cations were usually in the tetra- and octahedral state, Si–O-Co bonds characterized with cobalt coordination number of 2.1–2.3 have been generated. The Si–O-Co bonds can further be recrystallized to Co₃O₄ nanoclusters under extended crystallization condition, and the coordination number of cobalt increased to 3.7. In cyclohexane oxidation, the activation energy (<i>E</i>a) over cobalt decreased with the coordination number, the intracrystalline diffusion limitation was released by mesopores, and notably enhanced cyclohexane conversion (8.8%) and selectivity of cyclohexanol and cyclohexanone (KA oil, 91.2%) was achieved over the hierarchical Silicalite-1 with two-coordinated Co. Moreover, cyclohexyl hydroperoxide (CHHP) can in-situ be decomposed, and much more cyclohexanone can be produced with decreasing coordination number of cobalt, the CHHP selectivity decreased from 50% to less than 2.5%, while the ratio of cyclohexanol to cyclohexanone decreased from about 1.1 to 0.7. The catalytic stability was good, the KA oil selectivity and ratio of cyclohexanol to cyclohexanone remained almost the same after recycling seven times.</p>