Severe local acidosis causes tissue damage and pain, and is one of the hallmarks of many diseases including ischemia, cancer, and inflammation. A family of chloride channels activated by extracellular acidic pH has been implicated in acidosis-induced cell death by mediating Clˉ influx and subsequent cell swelling. PAC currents are widespread and display characteristic biophysical properties, including strong outwardly rectifying current-voltage (I-V) relationship, time-dependent activation at positive membrane potentials, and anion permeability sequence of Iˉ > Brˉ > Clˉ. The molecular identity of PAC was unknown until we recently identified a novel gene PACC1 (TMEM206) encoding the PAC channel. PAC shares no sequence homology to other membrane proteins, representing a completely new ion channel family. By performing cryo-EM and electrophysiology, we present two structures of human PAC, a high-pH (pH 8) resting closed state and a low-pH (pH 4) proton-bound non-conducting state, and reveal critical functional residues involved in pH-dependent activation and ion selectivity. We show a unique desensitization of PAC upon prolonged treatment at pH 4. The trimeric PAC contains a transmembrane domain (TMD) and an extracellular domain (ECD). We observed conformational change in the ECD-TMD interface and the TMD between the pH 8 and pH 4 structures. A titratable residue H98 from the ECD-TMD interface is involved in PAC pH sensing. The selectivity filter of PAC is located in the intracellular side of TM2, in which a charge reversal mutant (K319E) converts PAC to a cation-selective channel. Our data provide the structural basis to understand the proton-dependent gating mechanisms of PAC channel.