Molecular oxygen as a green, non-toxic and inexpensive oxidant has displayed lots of advantages compared with other oxidants towards more selective, sustainable, and environmentally benign organic transformations. The oxygenation reactions which employ molecular oxygen or ambient air as both an oxidant and an oxygen source provide an efficient route to the synthesis of oxygen-containing compounds, and have been demonstrated in practical applications such as pharmaceutical synthesis and late-stage functionalization of complex molecules. This review article introduces the recent advances of radical processes in molecular oxygen-mediated oxygenation reactions. Reaction scopes, limitations and mechanisms are discussed based on reaction types and catalytic systems. Conclusions and perspectives are also given in the end.