The invention belongs to the technical field of active substances of inorganic oxide of nickel, cobalt or ferrum, and particularly relates to a manganese cobalt composite oxide (MnCo2O4) magnetic nanocrystal and a preparation method thereof. The preparation method adopts a hydrothermal synthesis method and comprises the following steps of (1) weighing a certain amount of potassium permanganate, manganese acetate and cobalt acetate on the condition that a molar ratio of nKMnO4 to nMn(Ac)2 to nCo(Ac)2 is 2:3:10, adding pure water, uniformly stirring, obtaining a reaction mixture, (2) shifting the reaction mixture into a polytetrafluoroethylene-stainless steel high-pressure reaction kettle, sealing the high-pressure reaction kettle, placing in an oven, keeping warm at 150-200 DEG C for a certain time, conducting hydrothermal reaction for 10-24h, taking out the high-pressure reaction kettle, and (3) opening the high-pressure reaction kettle after cooling, conducting centrifugal separation on a reactant, using the pure water to wash a sample, obtaining a black precipitate, conducting vacuum drying, and obtaining the MnCo2O4 magnetic nanocrystal. The method is simple and easy, and the obtained MnCo2O4 magnetic nanocrystal is uniform in particle size, regular in shape, good in crystallinity, and controllable in atom proportioning and has a good magnetic property.