An integrated organic paddy farming system applies the concept of “Low External Input Sustainable Agriculture” (LEISA) in developing livestock and crop business in one area using local resources. This study is an attempt to analyze this farming system in Jetis, Paliyan, Gunung Kidul that has specific objectives to evaluate the farm management practices and to determine the optimal allocation resources use. The linear programming method was used to determine the optimal allocation of resources, while descriptive analysis was used to explain the practiced of this system in the study area. Primary data were collected from a farm survey and secondary data were obtained from relevant agencies.