Abstract In order to interpret the molecular structure and biological characteristics of Clostridium perfringens alpha‐toxin (CPA), the CPA251‐370 gene was cloned and the 120 amino acid carboxy terminal of CPA (CPA251‐370) was obtained. The secondary and three‐dimensional (3D) structures of CPA251‐370 were predicted. The secondary structure of CPA251‐370 consisted primarily of 35.48% β‐sheets and 44.35% random coils. Compared with the CPA toxin consisting of 10 α‐helices and eight β‐sheets, the 3D structure of CPA251‐370 only contained eight β‐sheets. The circular dichroism (CD) spectrum detection showed that the CD spectrum of CPA251‐370 changed slightly compared with the CD spectrum of CPA. Biological activity assays showed that CPA251‐370 had lost the phospholipase C (PLC) activity and haemolytic activity of CPA. More importantly, the mice immunized with CPA251‐370 were protected against a challenge with 1 MLD C. perfringens type A strain C57‐1. This study laid a solid foundation for explaining the relationship between molecular structure and biological characteristics of CPA in the future. Our research also provides CPA251‐370 as a candidate strains for genetic engineering subunit vaccines of C. perfringens type A.