Voltage-gated calcium (CaV) channels play essential roles in adjusting calcium influx upon membrane depolarization. CaV2 (N-, P/Q- and R-type) channels are concentrated in the presynaptic nerve terminals and important for the neurotransmitter release. Adjusting the presynaptic calcium channel gating exerts potent influence on synaptic plasticity. CaV channels need auxiliary subunits for proper trafficking to the plasma membrane and the channel gating. Especially CaVβ subunit plays crucial roles in the surface expression of CaV channels and fine-tuning of channel gating. It has been known that CaV channels are modulated by membrane phosphatidylinositol 4,5-bisphosphate (PIP2). The binding affinity between ion channel and PIP2 is important for the channel gating normally, but molecular mechanism of PIP2 regulation remains unclear. It was recently reported that subcellular localization of β subunit is a key factor for the control of PIP2 sensitivity of CaV channels. Here we found that the intracellular movement of I-II linker in a1 subunit is important for determining the PIP2 sensitivity of CaV channels. When the I-II linker was shifted to the plasma membrane, current inhibition by PIP2 depletion significantly decreased as like the responses triggered by membrane-tethered β subunit. Consistently we also found that inserting a flexible linker between membrane-tethered Lyn and GK domain of β subunit increased the PIP2 sensitivity of CaV channels. Polybasic motif at the C-terminal end of the I-II linker of CaV channels is a potential PIP2 interaction site. Neutralization of the polybasic motif of I-II linker abolished PIP2 sensitivity of CaV channels. Together, our results indicate that the conformational shift of I-II linker to the plasma membrane is the key mechanism for decreasing the PIP2 sensitivity of CaV channels and this shift is mainly regulated by auxiliary CaVβ subunit in physiological condition.