Transition delaying is of great importance for the drag and heat flux reduction of hypersonic flight vehicles. The first mode, with low frequency, and the second mode, with high frequency, exist simultaneously during the transition through the hypersonic boundary layer. This paper proposes a novel bi-frequency synthetic jet to suppress low- and high-frequency disturbances at the same time. Orthogonal table and variance analyses were used to compare the control effects of jets with different positions (USJ or DSJ), low frequencies (f1), high frequencies (f2), and amplitudes (a). Linear stability analysis results show that, in terms of the growth rate varying with the frequency of disturbance, an upstream synthetic jet (USJ) with a specific frequency and amplitude can hinder the growth of both the first and second modes, thereby delaying the transition. On the other hand, a downstream synthetic jet (DSJ), regardless of other parameters, increases flow instability and accelerates the transition, with higher frequencies and amplitudes resulting in greater growth rates for both modes. Low frequencies had a significant effect on the first mode, but a weak effect on the second mode, whereas high frequencies demonstrated a favorable impact on both the first and second modes. In terms of the growth rate varying with the spanwise wave number, the control rule of the same parameter under different spanwise wave numbers was different, resulting in a complex pattern. In order to obtain the optimal delay effect upon transition and improve the stability of the flow, the parameters of the bi-synthetic jet should be selected as follows: position it upstream, with f1 = 3.56 kHz, f2 = 89.9 kHz, a = 0.009, so that the maximum growth rate of the first mode is reduced by 9.06% and that of the second mode is reduced by 1.28% compared with the uncontrolled state, where flow field analysis revealed a weakening of the twin lattice structure of pressure pulsation.