The invention provides a construction method of a spray polyurea protection system for a concrete base surface. The construction method comprises the steps that a first primer layer, a first repair putty layer, a first polyurea spray layer, a second repair putty layer and a second polyurea spray layer coat the concrete base surface in sequence, wherein the first repair putty layer is formed by curing single-component polyurethane putty, and the single-component polyurethane putty is obtained by adding a latent curing agent for stirring and mixing when the content of isocyanate is up to 10%-15%by the reaction of polyols, isocyanate and a catalyst; and the surface defects of the first polyurea spray layer are repaired by the second repair putty layer, the second repair putty layer is formedby curing two-component polyurethane putty, the two-component polyurethane putty is composed of a component A and a component B, the component A is the single-component polyurethane putty, and the component B comprises 90.5-97.8 parts of polyaspartic acid ester.