  We study the thermodynamical phase structures of holographic QCD with
nontrivial topologically charged domain-wall/membranes which are originally
related to the multiple $\theta$-vacua in the large $N_c$ limit. We realize the
topologically charged membranes as the holographic D6-brane fluxes in the
Sakai-Sugimoto model. The D6-brane fluxes couple to the probe D8-anti-D8 via
Chern-Simon term, and act as the source for the baryonic current density of
QCD. We find rich phase structures of the dual meson system by varying
asymptotic separation of D8 and anti-D8. Especially, there can be a
thermodynamically favored and stable phase of finite baryonic current density.
This provides the supporting evidence for the discovery of the topologically
charged membranes found in the lattice QCD calculations. We also find a
crossover phase with the limiting baryonic current density and temperature
which suggest a Hagedorn-like phase transition of meson dissociation.
