The invention provides a method for treating water by the Fenton oxidization of activated molecular oxygen. In the method, transition metal ions, transition metal and transition metal oxides are used as activated molecular oxygen catalysts to generate hydroxyl radicals, so that organic matters in wastewater are removed by oxidization. Compared with a Fenton water treatment technology in which hydrogen peroxide is used as an oxygen source, the method has the advantages that: in a Fenton reaction of the activated molecular oxygen, molecular oxygen in air and oxygen are used as the oxygen sourcedirectly, so the oxygen source is wide, convenient and low in cost, and the water treatment cost is reduced greatly. The method for treating the water by the Fenton oxidization of the activated molecular oxygen is suitable for the treatment of various kinds of organic wastewater, high in durability and efficiency, is environment-friendly and easy to operate, does not have secondary pollution, meets the requirement of actual water treatment units, and has large application potential in the field of environmental pollution regulation.