The purpose of this study is to improve the ammonia (NH3) emission inventory estimation in the domestic CAPSS (Clean Air Policy Support System). Currently, the ammonia emissions rate is obtained by multiplying the activity (number of livestock) by emission factors. The amount of movement and treatment are not considered in the estimation of ammonia emission rates. However, livestock manure is currently moved and treated in accordance with the energy recycling policy. In this study, the new emission estimation method were suggested considering the moving and treatment characteristics of livestock manure. A new ammonia emissions was calculated for Bcity and Y-gun at Chungcheongnam-do province. It was shown that the moving and treatment ratio of ammonia emissions were 4.3% and 8.4%, respectively. Furthermore, this ratio would be increased rapidly with the continuous establishment of large-scale manure treatment facilities.