The invention provides the preparation method of a water intermediate coating suitable for automobile factories and repair. The coating prepared by the method is universally suitable for automobile factories and repair. The preparation method comprises the following steps and process conditions: (1) synthesizing water-dispersible resin; (2) modifying hydrophilic polyisocyanate; (3) preparing the intermediate coating for automobile factories and repair; and (4) mixing the intermediate coating prepared in step (3) with the hydrophilic end-terminated polyisocyanate synthesized in step (2) to obtain the final product. The prepared intermediate coating has high applicability and is suitable for factory manufacturing and for repair. The intermediate coating is very friendly to the environment and greatly reduces the use of and the dependence on organic solvent, thus effectively conserving the energy resources. Additionally, the coating has the advantages of excellent flexibility, particularly high chip resistance and water resistance, smooth and fine coating surface and excellent interlayer adhesive force with the prime coat and the top coat.