The holographic entanglement entropy of an infinite strip subsystem on the asymptotic AdS boundary is used as a probe to study the thermodynamic instabilities of planar R-charged black holes (or their dual field theories). We focus on the single-charge AdS black holes in $D=5$, which correspond to spinning D3-branes with one non-vanishing angular momentum. Our results show that the holographic entanglement entropy indeed exhibits the thermodynamic instability associated with the divergence of the specific heat. When the width of the strip is large enough, the finite part of the holographic entanglement entropy as a function of the temperature resembles the thermal entropy, as is expected. As the width becomes smaller, however, the two entropies behave differently. In particular, there exists a critical value for the width of the strip, below which the finite part of the holographic entanglement entropy as a function of the temperature develops a self-intersection. We also find similar behavior in the single-charge black holes in $D=4$ and $7$.