Remanufactured engine crankshaft axial clearance is an important factor which affects the remanufactured engine quality. Besides, the control of crankshaft axial clearance is the difficult part during the assembling process of remanufactured engine under the uncertain environment. The factors affecting the remanufactured engine crankshaft axial clearance in uncertainty are analyzed. The uncertainty measure model is put forward based on the assembly size of information entropy. According to this mode, the quality coupling relationship of crankshaft axial clearance during the assembling process of the remanufactured engine is researched. On the condition that the assembly size entropy of the crankshaft axial clearance of the remanufactured engine is not to be bigger than that of the original product, the coefficients of the first axle journal’s width of the remanufactured crankshaft and the bearing pedestal for cylinder block are deduced by mathematical formulas. The optimal control method of crankshaft axial clearance of the remanufactured engine is proposed, which is based on the group mating model. This method is applied on the manufacturing process of a remanufactured engine company, to verify that the proposed method can make best use of remanufacturing resources, and improve the quality of remanufacturing products.