Thermal induced reliability issues in ultra-high density storage arrays are becoming increasingly significant, especially in 3D stacks. In this paper, research into the reliability issues of a stacked 3D TaOx vertical resistive random access memory (VRRAM) is demonstrated first through experiments. The results indicate that the thermal induced reliability issues of a 3D VRRAM are very severe. To further study the thermal effect and its impact on a 3D VRRAM, finite element analysis models of the 3D VRRAM are established in CMOSOL Multiphysics. Parameters including different feature sizes (F), metal layer thickness (tm), isolation layer thickness (ti) and the number of stacked layers (Ns) are simulated and investigated to clarify the relationship between heat dissipation performance and the device’s integration density. In addition to this, the influence of electrode materials is also discussed. The results reveal that scaling down F and tm are the main reasons for bad heat dissipation performance, and optimizing the thermal conductivity in both electrodes and the isolation layer can improve the heat dissipation performance. In addition, a comparative investigation into the heat dissipation performance in a 3D horizontal RRAM (HRRAM) has also been performed under the same conditions. Finally, by evaluating the influence of the integration parameters on the thermal effect related reliability performance, design guidelines for a 3D VRRAM and HRRAM are proposed.