The CFD fluid analysis software STAR-CCM+ is chosen to conduct the flow field analysis and structural improvement of motorcycle engine cooling jacket. Results show that the unreasonable layout of cylinder holes in the original scheme of water jacket leads to poor flow uniformity, poor cooling in the high temperature area at the exhaust side and the spark plug side, which is not conducive to the cooling of high temperature area. After reducing the flow area of cylinder hole on the intake side in the original water jacket scheme, the flow velocity of coolant on the exhaust side and the spark plug side was significantly increased, and the utilization rate of the coolant was improved, which ensured the effective cooling of high temperature area. The experimental results show that cylinder temperature of the engine with the improved cooling water jacket structure decreased by 8 degrees, which indicates that the improved cooling water jacket structure is effective and the cooling performance is significantly improved. The research method and results can provide theoretical reference for the structural design of motorcycle engine cooling water jacket.