In this paper, we derive the universal (cut-off-independent) part of the holographic entanglement entropy in the noncommutative Yang-Mills theory and examine its properties in detail. The behavior of the holographic entanglement entropy as a function of a scale of the system changes drastically between large noncommutativity and small noncommutativity. The strong subadditivity inequality for the entanglement entropies in the noncommutative Yang-Mills theory is modified in large noncommutativity. The behavior of entropic $c$-function defined by means of the entanglement entropy also changes drastically between large noncommutativity and small noncommutativity. In addition, there is a transition for the entanglement entropy in the noncommutative Yang-Mills theory at finite temperature.
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