N-type voltage-gated calcium (CaV) channels mediate Ca2+ influx at the presynaptic terminals in response to action potential and play vital roles in synaptogenesis, neurotransmitter releasing, and nociceptive transmission. Ziconotide is a N-type calcium channel blocker and was regarded as an analgesic agent for the amelioration of chronic pain. Here we elucidate a cryo-electron microscopy (cryo-EM) structure of the apo and ziconotide-bound human CaV2.2 complex at near-atomic resolution. This complex structure reveals how the CaV2.2, β1, and α2δ1 subunits are assembled, and unraveled the novel binding fashion of ziconotide to CaV2.2. In our structures, the second voltage-sensing domain (VSD) is trapped by a PIP2 molecule and stabilized at a resting-state conformation, which is distinct from the other three VSDs of CaV2.2 as well as activated VSDs observed in previous structures of CaV channels. The structures also shows that the intracellular gate formed by S6 helices is closed, and a W-helix from the DII-III linker is determined to act as a blocking-ball that causes closed-state inactivation in CaV2.2. The ziconotide is docked above the selectivity filter of CaV2.2, harbored by the negative-charged extracellular doom fabricated by α2δ1, and thus blocks the entrance of calcium ions. Collectively, our structure provides previously unseen structural insights into fundamental gating mechanisms of CaV channels and demonstrated the molecular basis of the analgesic effect of ziconotide.