We consider the noncommutative deformation of the finite temperature holographic QCD (Sakai--Sugimoto) model in external electric and magnetic field and evaluate the effect of the noncommutaivity on the properties of the conductor-insulator phase transition associated with a baryon number current. Although the noncommutative deformation of the gauge theory does not change the phase structure with respect to the baryon number current, the transition temperature $T_{c}$, the transition electric field $e_{c}$ and magnetic field $b_{c}$ in the conductor-insurator phase transition depend on the noncommutativity parameter $theta$. Namely, the noncommutativity of space coordinates has an influence on the shape of the phase diagram for the conductor-insurator phase transition. On the other hand, the allowed range of the noncommutativity parameter can be restricted by the reality condition of the constants of motion.
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