Aiming at the difficulty of control and evaluation of main bearing deformation in the coordination design of the main bearing assembly structure for a high-speed diesel engine, taking MRD (the MRD means the maximum radial deformation of the bearing bush) of the bearing bush as an index to evaluate the out-of-round deformation of the bearing bush was proposed in this paper. The numerical calculation method of the MRD was given and the correctness of the method was experimentally verified. And the influence rules of different design parameters on the MRD were analyzed. On this basis, the coordination multi-objective optimization research of the main bearing assembly structure was carried out, and the optimization results were analyzed based on the influence rules of different design parameters on the reliability indexes. The results show that, when the pre-tightening force of the vertical bolt and the bearing bush interference are 240 kN and 0.17 mm respectively, the MRD reaches the minimum value. If the two values continue to increase, redundant loads can be generated, leading to the increase of the MRD. After optimization, the engine block strength coordination and bearing cap strength coordination had increased by 2.47% and 10.48%, respectively, and the deformation coordination and contact coordination had increased by 46.15% and 14.84%, respectively.