The integrated permit system is applied to class 1 and 2 atmospheric and water pollutant discharge facilities in 19 sectors. The fertilizer sector should receive a permit for a period of four years, from 2019 to 2023. The purpose of this study is to investigate the differences between the Korean Best Available Techniques (BAT) reference document (K-BREF) and the European Union BAT reference document (EU-BREF) in terms of the process and emission characteristics of fertilizer manufacture. K-BREF is written by focusing on products, whereas EU-BREF is produced on focusing on manufacture process. There are five types of BATs(best available techniques economically achievable) in Korea. These BATs selected mainly to recover and reuse raw meterials and save energy. The number of BATs and BAT-AELs(BAT associated emission level) in K-BREF is smaller than that in EU-BREF. We suggest that BATs and those environmental management parameters in Korea need to further reflect the emission characteristics in the fertilizer sector.