In this study, the effects of entropy layer on the boundary layer over hypersonic blunt cones for a thermochemical equilibrium gas are investigated. The flow and stability characteristics of the entropy and boundary layers are presented considering the chemical reactions. It is found that the entropy layer has little influence on the inner layer inside the boundary layer. The inner layer thickness increases when chemical equilibrium is considered, which stems from the enhanced viscosity protection near the wall surface. At the leading edge of the blunt cone, due to the effects of the equilibrium gas, the temperature in the boundary and entropy layers decreases and the boundary-layer-edge parameters significantly change. The entropy layer gradually vanishes along the downstream direction, and the effects of chemical reactions are concentrated in the boundary layer. The entropy swallowing point of the equilibrium gas does not significantly differ from that of the perfect gas. For all the analyzed cases, chemical reactions stabilize the entropy layer instability modes. The instability region and the frequency range of the equilibrium gas decrease, and the growth rate of the most unstable perturbation of the equilibrium gas is considerably smaller than that of the perfect gas. Moreover, the results show that the equilibrium gas has a minor influence on the process of the blunt cone boundary layer solution tending to the sharp cone solution.