The magnetosphere undergoes a transition from a dipole-like to taillike structure in the antisunward direction. In this region, Alfvén ballooning instability has been considered as a leading candidate to be responsible for the onset and expansion phase of observed impulsive substorms. We apply the generalized Ohm's law in isotropic Hall-MHD equations and study the effect of heat flux on the ballooning modes under substorm circumstances. The set of partial differential equations is obtained for a general ballooning dispersion relation from which all classical Alfvén waves and fundamental ballooning modes are recovered, e.g., the decoupled shear Alfvén and magnetosonic modes, the classical ballooning instability in incompressible plasmas. In the absence of the heat flux, the ballooning mode is featured by the coupling of the two modes by the superposition of the independent Hall effect and the independent plasma inhomogeneity effect. By contrast, heat flux exerts its influence on the ballooning mode by updating the coefficients of the terms in the dispersion relation. The results expose that the growth rate ( BM ) has two branches. If k p is free, one branch shifts versus , while the other branch is damped substantially by the heat flux, leading to a more stable ballooning mode; if k c is free, one branch shifts little versus , but the other one has higher BM driven by the heat flux, leading to a more unstable ballooning mode.