Human lifestyle is affected by the agricultural development in the last 12,000 years ago. The development of agriculture is one of the reasons that global population surged. To ensure sufficient food production for supporting human life, pesticides as a more effective and economical tools, are extensively used to enhance the yield quality and boost crop production. This study investigated the factors that affect crop production and whether the factors of pesticide usage are the most important factors in crop production using the dataset from Kaggle that provides information based on crops harvested by various farmers. Logistic regression is used to investigate the relationship between various factors and crop production. However, the logistic regression is unable to deal with predictors that are related to each other and identifying the greatest impact factor. Therefore, causal discovery is applied to address the above limitations. The result of causal discovery showed that crop condition is greatly impacted by the estimated insects count, where estimated insects count is affected by the factors of pesticide usage. This study enhances our understanding of the influence of pesticide usage on crop production and contributes to the progress of agricultural practices.