Asymmetric synthesis of chiral epichlorohydrin (ECH) from 1,3-dichloro-2-propanol (1,3-DCP) using halohydrin dehalogenase (HHDH) is of great value due to the 100% theoretical yield and high enantioselectivity. In this study, HheC (P175S/W249P) was immobilized on an A502Ps resin and used for the preparation of (S)-ECH. In aqueous system, the immobilized HheC catalyzed the biosynthesis of (S)-ECH with 83.78% yield and 92.53% enantiomeric excess (ee) at 1,3-DCP concentration of 20 mM. The non-aqueous system was further developed using water saturated ethyl acetate as solvent and reaction phase. The non-aqueous bioconversion system showed higher enantioselectivity (> 98% ee) toward (S)-ECH production with modest conversion (52.34%) compared with ever reported aqueous reactions. Batch reactions were performed in a packed-bed bioreactor for 45 batches in aqueous phase and 24 batches in non-aqueous phase. The present work demonstrated the potential of immobilized HheC (P175S/W249P) in aqueous and non-aqueous phase biosynthesis of chiral ECH.