In order to effectively suppress the seal failure caused by the deformation of cylinder liner after improving the explosion pressure of diesel engine cylinder, the variation laws of cylinder liner displacement, cylinder liner section deformation and cylinder liner stop flatness for a 3-cylinder turbocharged diesel engine with small displacement before and after the supercharging were compared and analyzed with the CAE analysis method based on the multi-body dynamics theory, and the feasible schemes and measures for controlling cylinder liner deformation were proposed. The results show that the deformation is large in the upper part and small in the lower part of cylinder liner before and after using the supercharging technology. The deformation of each cylinder liner lengthens along the Y axis and shortens along the X axis. The deformation of the second cylinder is relatively large and the deformation of the first cylinder is relatively small. The deformation fluctuation of the top part of each cylinder sleeve is more severe and the deformation value is larger. Compared with the 3-cylinder non-supercharged diesel engine, the supercharging technology has minor influence on the radial deformation of each section of cylinder liner. The unevenness of cylinder liner lip for the three cylinders reduces by about 35.5%, 23.2% and 26.6% respectively. After using the bolt structure of cylinder head with deep countersunk hole, the bolt is lengthened, the compressive stress of body part above the counterbore is released, the corresponding deformation is reduced, and the deformation of cylinder liner can be inhibited effectively.