The flow separation occurring in the S-shaped diffuser with boundary layer ingestion (BLI) has a significant effect on the performance of the embedded engine. Previous studies have found that the area ratio (AR) as well as the length-to-offset ratio (LOR) of the S-shaped diffuser are the key contributing factors that affect the flow separation features. Based on the flow phenomena observed in previous studies of an S-shaped diffuser with 100% BLI, a hypothesis that the parameter height-to-radius ratio (HRR) may also have significant effect on the flow separation features in the S-shaped diffuser is proposed. The purpose of this paper is to verify this hypothesis and to further investigate the effect of HRR on the flow separation features in the S-shaped diffuser with BLI using numerical methods. First, the hypothesis that HRR has an effect on the flow separation features in the S-shaped diffuser is verified under uniform inlet condition. Second, the effect of HRR on the flow separation features is investigated under different relative heights of inlet BLI. It is found that the flow separation features in the S-shaped diffuser are very sensitive to the change in HRR but not to the change in relative height of inlet BLI. Finally, for the fixed boundary layer height generated from the airframe, the S-shaped diffuser with a smaller design HRR can significantly suppress the flow separation and thus achieve a higher total pressure recovery and a lower distortion coefficient. The results provide improved understandings of the factor affecting the flow separation features in the S-shaped diffuser, and are useful for improving the aerodynamic performance of the embedded engine with BLI.