From the perspective of green chemistry and sustainable development, it is highly desirable to produce catalysts in an environmentally friendly manner and utilize them to activate O2 for converting cheap chemicals into value-added chemicals. In this work, we have synthesized two cobalt-based metal-organic frameworks (Co-MOFs) in ethanol, a non-toxic reaction medium, and used them to convert isochromans to isochromanones with O2 as an oxidant and needing no additives. The experimental results indicate that the two Co-MOFs exhibit a favorable catalytic performance, in which the 2D Co-MOF (1) possesses a higher catalytic activity than the 3D Co-MOF (2). This may be due to the enhanced catalytic site exposure and rapid substance, electron, and proton transfer within the 2D Co-MOF. Furthermore, the reaction mechanism analysis indicates that the catalytic process may involve a radical reaction pathway. This work serves as an invaluable interpretation for advancing alternative 2D Co-MOF for activating O2 in organic catalytic transformation.