This paper is the first investigation on the effect of flow control methods on the part load performance in a spark ignition engine. For comparison of the methods, two control devices, port throttling and masking, were applied to a conventional engine without any design change of the intake port. Steady flow evaluation shows that steady flow rates per unit opening area and swirl ratio are very low compared with the port throttling and saturated from mid-stage valve lift, however, swirl increases slightly as the lift is higher in case of 1/4 masking control. In the part load performance, the effect of simple port throttling on lean misfire limit expansion is limited and insufficient; on the other hand a masking improves the limit considerably without any port modification for increasing swirl. Also the results show that the intake flow control improves the combustion with following two mechanisms: stratification induced by the combination of the flow pattern and the fuel injection timing attribute to ignition ability and the intensified flow ensure fast burn. In addition fuel consumption reduces under the flow controls and the reduction rate is different according to the operation conditions and control methods. At the Stoichiometric and/or low speed and low load the throttling method is more advantageous; however vice versa at lean and high load condition. Finally, the throttling is more efficient for HC reduction than masking, on the other side the NOx emissions increase under the masking and decrease under the port throttling compared with conventional port scheme.