The stiffness of the main bearings of a diesel engine is the research that has been focused on due to the fact that traditional evaluation indexes can hardly accurately characterize the coordinated deformation of the crankshaft and the bearing shell. Regarding the clearance margin that could judge whether motion interference occurs between the main bearing shell and the crankshaft journal after deformation as the evaluation index, the characterization method of for diesel engine main bearings based on the evaluation index and the numerical calculation method for the main bearing clearance are proposed. Experiments are designed and conducted to verify the feasibility and accuracy of the evaluation index. The results show that it is feasible to take the main bearing clearance as the evaluation index of the coordinated deformation. The relative errors between the calculation results and the measurement data of the centripetal radial deformation of the main bearing shell in the preload condition are less than 7%, indicating the accuracy of the computational method. This research provides theoretical basis for main bearing stiffness reliable design of HDP diesel engine.