The intake uniformity of manifold is an important performance index of engine and the simulation and calculation is an important method for its optimization. Whether the simulation process is reasonable or not has a great influence on the calculation results. Two intake manifolds were respectively optimized and accepted with star-ccm+ software based on the intake uniformity by using the industrial most commonly used calculation model and condition. Then the comparison of intake uniformity difference was conducted after introducing factors such as different mass flow rates, different throttle angles and inlet pipes and the more accurate model was further analyzed. The calculation results and established model were reliable according to the measured flow coefficient deviation on the steady flow test bench. It was concluded that the single mass flow or pressure difference is reasonable to be taken as input of simulation through further combining with computational fluid field and fluid theory. The factors of inlet structure had a great influence on the uniformity calculation, which were close to the actual and included throttle angle and inlet elbow before the throttle. Considering these factors, the unevenness within 1% optimized with the initial model would worsen by 3-10 times. In addition, the length of straight line before or after the throttle also had influence on the uniformity.