Coccidiosis is a kind of disease in chickens, which has a serious economic impact on poultry production worldwide. In this experiment, the 3-1E gene from Eimeria acervulina was amplificated by RT-PCR. The target gene was linked to pPICZαA vector, then electrotransformed into Pichia pastoris. The secreted recombinant protein expression was induced by methanol, and the recombinant 3-1E protein was obtained every24hours post induced, then it was identified by SDS-PAGE and Western Blot. The protein was purified using the His-tagged protein purification kit and its concentration was determined by Bradford method using a protein quantitation kit. This study laid a foundation for the vaccine production and the evaluation of vaccine efficacy.