The invention discloses a preparation method and application of a core-shell structural magnetic nano composite catalyst. The method comprises the following steps: step 1, dissolving a metal salt X containing Fe<2+> and a metal salt Y containing Co<2+> into deionized water, and performing uniform stirring to obtain a mixed liquid A; step 2, removing dissolved oxygen in the mixed liquid A by ultrasonic vibration or suction filtration to obtain a mixed liquid B; step 3, adding a NaOH solution dropwise into the mixed liquid B to obtain a mixed liquid C; step 4, performing reflux on the mixed liquid C under heating and stirring, allowing the liquid to stand, taking out a product, performing alternated washing for a plurality of times by using deionized water and absolute ethanol, performing drying, and performing grinding to obtain a powdery magnetic cobalt iron hydroxide; and step 5, performing calcination on the powdered magnetic cobalt iron hydroxide, performing grinding, and performingsieving to obtain the core-shell structural magnetic nano composite catalyst using Co3O4 as a shell and CoFe2O4 as a core. The preparation method provided by the invention has a simple and easily-operated process, and can realize microscopic regulation on the morphology of the composite catalyst, and forms a core-shell structure, thereby facilitating electron transfer in a catalytic reaction process.