Starting with arXiv:1104.2843 [hep-th], which presents a top-down approach to holographic superconductor using an intersecting brane configuration in Witten-Sakai-Sugimoto model at finite density, we consider a toy configuration of intersecting D3-branes to model the above brane configuration and analyse its thermal stability in Yang-Mills approximation. We further extend the calculation to consider intersecting stacks of D-branes at finite temperature. A different brane configuration is then proposed, that could arise in the context of arXiv:1104.2843 [hep-th]. We then study and compare various phases of the holographic QCD model at finite baryon number and isospin chemical potential.