The invention discloses a preparation method of a micro-molecular organic acid preparation microcapsule sustained release agent. The preparation method includes the steps: (1) heating main materials in a reaction kettle to a molten state; (2) adding carriers into the materials, and stirring the materials to form a mixed state; (3) heating auxiliary materials to melt, and sufficiently and uniformlystirring melted auxiliary materials; (4) mixing the main materials and the auxiliary materials, and cutting and uniformly mixing mixture in the heat insulation state; (5) transferring the materials into a storage tank in the heat insulation state; (6) performing spraying granulation on the materials in the storage tank; (7) collecting and screening made microcapsule particles; (8) inspecting content and indexes of components, and packaging the agent. Products produced by the method can effectively control release positions in animal digestive tracts, more excellent comprehensive titer is achieved, and the products can be used in various environments such as premixed materials.