The invention provides a Fe3O4/GQD nano catalyst as well as a preparation method and application thereof. A ferroferric oxide modified graphene quantum dot is prepared by using a coprecipitation method, and has good stability. Through a Fenton reaction, low-concentration organic pollutants such as dyes, pesticides and hormones, long-lasting organic pollutants, and the like in water can be subjected to effective catalytic degradation. The nano catalyst provided by the invention is simple in preparation method, low in cost and feasible in large-scale preparation, has the characteristics of efficient catalysis activity and the like, and has the potential of being applied to purification of low-concentration refractory organic wastewater.