Beryllium is a very important strategic metal and has been applied in high-tech industries. Since the low beryllium content in minerals, the enrichment technique is a vital aspect of beryllium smelting. In this study, we present a novel protic ionic liquid, 4-Hydroxymethyl-5-methylimidazolium p-Chlorobenzoate ([Hymim][pCb]), as an efficient and environmentally friendly extraction solvent for beryllium preconcentration in aqueous solution. Our research demonstrates that Be II can be captured rapidly with high efficiency, reaching nearly 99.6% within 2 h. By controlling the initial metal concentration and pH condition, we could achieve the selective extraction of beryllium in the presence of other heavy metal ions. Our findings also shed new light on the extraction mechanism established by the material characterizations and density functional theory (DFT) calculation, revealing that metal ions disrupt the proton transfer between the cation and anion in the ionic liquid, leading to metal chelation with the cation and subsequent translation of the anion into an aqueous solution. Overall, our research presents a novel method for the enrichment of beryllium in the smelting process while also expanding the scope of protic ionic liquid applications. The efficient and selective extraction of beryllium demonstrated in this study holds great promise for the advancement of beryllium-related industries.