The stability of a hypersonic boundary layer on a flared cone was analysed for the same flow conditions as in earlier experiments (Zhang et al., Acta Mech. Sinica, vol. 29, 2013, pp. 48–53; Zhu et al., AIAA J., vol. 54, 2016, pp. 3039–3049). Three instabilities in the flared region, i.e. the first mode, the second mode and the Görtler mode, were identified using linear stability theory (LST). The nonlinear-parabolized stability equations (NPSE) were used in an extensive parametric study of the interactions between the second mode and the single low-frequency mode (the Görtler mode or the first mode). The analysis shows that waves with frequencies below 30 kHz are heavily amplified. These low-frequency disturbances evolve linearly at first and then abruptly transition to parametric resonance. The parametric resonance, which is well described by Floquet theory, can be either a combination resonance (for non-zero frequencies) or a fundamental resonance (for steady waves) of the secondary instability. Moreover, the resonance depends only on the saturated state of the second mode and is insensitive to the initial low-frequency mode profiles and the streamwise curvature, so this resonance is probably observable in boundary layers over straight cones. Analysis of the kinetic energy transfer further shows that the rapid growth of the low-frequency mode is due to the action of the Reynolds stresses. The same mechanism also describes the interactions between a second-mode wave and a pair of low-frequency waves. The only difference is that the fundamental and combination resonances can coexist. Qualitative agreement with the experimental results is achieved.