The high degree of centerline curvature and cross-stream pressure gradient in S-inlet ducts gives rise to boundary layer separation and secondary flows, which result in poor pressure recovery and non-uniform flow in the outlet interface with the engine. The flowfield in ducts is three-dimensional due to the existence of secondary flow, so ordinary two-dimensional actuations have poor effect on reforming the flow. Synthetic jet actuations extended in different spanwise positions were employed to manipulate the flow, and compared with the two-dimensional actuation, The interaction mechanics between flow separation and secondary flow was studied at first. It was found that the secondary flow enhanced Ol~ weakened flow separation depending on the spanwise position of synthetic jet actuators. Moreover, the J flow separation enhanced the secondary flow, thus causing lower pressure recovery and flow distortion in the duct outlet. The actuators located at different spanwise positions will weaken the secondary flows by improving the flow separation to get energetic and uniform main flow.