Based on the gauge-gravity duality, we study the three-dimensional QCD (QCD3) and Chern-Simons theory by constructing the anisotropic black D3-brane solution in IIB supergravity. The deformed bulk geometry is obtained by performing a double Wick rotation and dimension reduction which becomes an anisotropic bubble configuration exhibiting confinement in the dual theory. And its anisotropy also reduces to a Chern-Simons term due to the presence of the dissolved D7-branes or the axion field in bulk. Using the bubble geometry, we investigate the ground-state energy density, quark potential, entanglement entropy and the baryon vertex according to the standard methods in the AdS/CFT dictionary. Our calculation shows that the ground-state energy illustrates degenerate to the Chern-Simons coupling coefficient which is in agreement with the properties of the gauge Chern-Simons theory. The behavior of the quark tension, entanglement entropy and the embedding of the baryon vertex further implies strong anisotropy may destroy the confinement. Afterwards, we additionally introduce various D7-branes as flavor and Chern-Simons branes to include the fundamental matter and effective Chern-Simons level in the dual theory. By counting their orientation, we finally obtain the associated topological phase in the dual theory and the critical mass for the phase transition. Interestingly the formula of the critical mass reveals the flavor symmetry, which may relate to the chiral symmetry, would be restored if the anisotropy increases greatly. As all of the analysis is consistent with characteristics of quark-gluon plasma, we therefore believe our framework provides a remarkable way to understand the features of Chern-Simons theory, the strong coupled nuclear matter and its deconfinement condition with anisotropy.