This paper examines the effect of unstable thermal stratification on vortex breakdown in Vogel-Escudier flow. A three-dimensional direct numerical simulation of Navier-Stokes and energy equations are used to simulate a flow inside a cylindrical container generated by rotating the top lid. The top and bottom are kept at two constant temperatures such that unstable stratification is maintained. The rotation speed is related to the Reynolds number (Re), and buoyancy is linked to the Rayleigh number (Ra). The streamline and vertical velocity contour plots indicate different regimes of the flow depending on the Re and Ra. The convection dominated (CD) regime has a characteristic large-scale circulation similar to the Rayleigh-Bénard convection, and the rotation dominated (RD) regime has a central axial vortex and breakdowns. A transitional regime between RD and CD regimes is also identified from energy consideration. The influence of Ra on a vortex breakdown bubble and its relation to azimuthal vorticity is investigated in detail. Consistent with the literature on Vogel-Escudier flow, the azimuthal vorticity is shown to be essential for the breakdown in the presence of buoyancy as well. In the low Re limits, the energy of flow tends to be associated with the r-z plane velocity field, while at large Re, the energy is associated with the out-of-the-plane velocity field. Thermal plumes align along the axis for large rotations and are affected by the vortex breakdown bubble. The velocity perturbation structures and plumes show a remarkable distinction between rotation and convection-dominated regimes in the topology. © 2021 Author(s).