The intake port flow characteristics in an internal combustion engine significantly affect its power output, fuel economy, and emissions. To optimize the flow characteristics in the intake port, increasing attention has been paid to its design process. However, the casting and machining processes of the intake port are underappreciated, which may introduce significant deviations, leading to undesirable variation of intake port flow and subsequent deterioration in engine combustion and emissions. In this paper, steady flow tests were carried out on a four-valve diesel engine to investigate how and to what extent the casting and machining deviations of the intake port influence the in-cylinder flow characteristics. The results show that these deviations lead to the variation of swirl ratio up to 20%. Then, computational fluid dynamics (CFD) simulation was conducted for understanding the reason. It is indicated that higher tolerance is needed during the casting and machining processes. For example, in order to control the variation of swirl ratio within 10%, the inclined angle should be controlled at less than 1 deg, the eccentric distance should be restricted to less than 0.5 mm, and the swelling thickness should be limited to less than 1 mm.