A three-dimensional self-throttling system is proposed in a scramjet combustor with transverse fuel jet, and investigated by Reynolds-averaged Navier-Stokes(RANS) simulations with the k-ω SST turbulence model. Numerical validation has been carried out against experiment and LES results. The effects of the jet-to-cross-flow momentum flux ratio and the throttling angle on mixing performance, fuel jet penetration depth and total pressure losses are all addressed. Through the proposed throttling system, the higher pressure upstream of the transverse fuel injection can drive part of the low momentum mainstream air into the downstream lower pressure region. The flow structures and the interactions between the shock waves and boundary layer are significantly modified to improve the mixing performance. The enhancement of mixing efficiency in the self-throttling system is closely related to the magnitude of the jet to crossflow momentum flux ratio, and a smaller throttling angle is found to further improve the mixing. On the other hand, the self-throttling system has a good performance in reducing the total pressure losses.