Scorpion venom contains a considerable variety of neurotoxic peptides that can act on ionic channels. Here, we describe an orthogonal 2D-reversed phase/hydrophilic interaction chromatography system (RPLC/HILIC) and use it to separate short-chain peptides from Asian scorpion Buthus martensi Karsch (BmK) venom in a high throughput format. Due to its high orthogonality and efficiency, 18 homogenous peptides were purified and sequence identified by MS/MS with collision-induced dissociation. Among them, four peptides were discovered, which only have evidence at transcript-level, were first purified from crude venom in this study. Two peptides named BmKK2-b and Martentoxin-b were found the new cleaved chains of known BmKK2 and Martentoxin. In addition, two novel peptides named BmKK12 and BmKK16 in this paper were sequenced by de novo MS/MS, which we predict, are members of potassium channel toxin α-KTx 17 subfamily by homology to other known peptides found in the Swiss-Prot protein database.