Data Mining is a process of discovering knowledge or rules from available dataset. It is possible to make optimized production environment based on association rules mined from production data through association rule mining system. During the production process of Bio-chemical enterprises, it is expected that the environment such as temperature, water condition and raw material supply are appropriate to obtain best production output. However, due to the complexity of production, it is not easy to acquire the optimized condition. This paper therefore tries to design and develop a knowledge discovery software program intending to provide such tools. The paper also analyzes index segmentation and association rule mining from rare transactions from large dataset based on relative supporting value, which is illustrated in detail. The developed system was tested and verified in practice, which proves that the system can be applied in Bio-chemical production data analysis.