Agricultural ecosystem biodiversity monitoring and community variation analysis of insects were conducted from 2016 to 2018 in selected conventional and organic farming fields in Goesan district, Chungcheongbuk-do, South Korea. The total number of 1,125 species in 16 orders and 207 families were identified. The numbers of species collected in the locations practicing organic farming were greater than the conventional farming both in the paddy fields (564 vs. 383 species) and the upland fields (471 vs. 365 species). Among them, Hemiptera had the most abundant of species, followed by Diptera, Hymenoptera, Coleoptera and Araneae. We calculated various index values of biodiversity (diversity index H’, richness index R, evenness index J’, dominance index D, and similarity index QS) based on quantitative measurements of species and individuals collected over three years of field monitoring. Variations in biodiversity index values in different agricultural systems show that the positive effect of organic farming is to produce more biodiversity than conventional farming systems. When compared to other index results reported in Korea, Japan and China, the richness index was higher and other index values were at similar levels.