Intake is not only the main air supply component of an aircraft, but also one of the forward radar scattering sources. The aerodynamic and stealth performance of intake is critical to the serviceability of advanced fighter aircrafts. The effects of baffle boards with different configurations on the performance of the caret intake with a double S-duct diffuser are presented in this article. The multi-level fast multipole method (MLFMM) and the SST k-ω turbulence model were respectively used to calculate the surface current and the flow field. It was found that the average RCS value of intake can be effectively reduced by installing the baffle board with vertical orientation in the front diffuser, with the DC60 value and the loss of outlet total pressure both increased slightly. The boundary layer separation and the RCS characteristics of intake were closely related to the configuration of the corrugated baffle board. Compared with the traditional curved board, by installing the corrugated board with optimized corrugation number and shape, the stealth performance of intake can be further improved, and the loss of aerodynamic performance can be also reduced.