This study presents a numerical investigation of suction control in an aggressive S-shaped air intake with large boundary ingestion. The results show that the variation of suction control parameters such as suction location, suction pipe diameter, and suction angle all have an impact on the effectiveness of the flow control. In general, further upstream suction, such as near the throat, is favorable for the decrease of the second flow intensity and the area of the low-energy fluid region at the exit of the S-shaped inlet. However, it is bad for the total pressure recovery and the circumferential total pressure uniform distribution. From the perspective of the uniformity of the total pressure distribution at the air intake exit, there is an optimal location for suction between the throat and the separation start point. A bigger suction pipe diameter brings better effects as the suction location and suction angle keep constant, due to more low-energy fluid being sucked out. But this doesn’t mean the largest mass flow suction results in the biggest improvement. Overall, sucking at the 1st bend, with suction angle and suction pipe diameter equaling 15 degrees and 12 mm, respectively, is the optimal suction scheme here. Since the change rule of the cross-section area along the centerline has not changed during suction control, the second flow and complex surface streamline at the air intake exit cannot be eliminated, though they can be decreased a lot with reasonable suction control. Similarly, owing to large boundary ingestion, the remarkable low-energy fluid region always exists despite the significant reduction of the separation and second flow, which is very different from the results of this kind of micro-suction executed in the non-BLI S-duct. To pursue a higher improvement, suction combined with vortex generator vanes has been further studied. Corresponding results analysis shows that the hybrid flow control method has great potential and should be investigated in detail in the future.