This paper investigates the potentially positive effects of internal auditing on the performance of the Credit Department of Farmers' Association (CDFA) in Taiwan. The empirical model of operating performance for CDFA is established by combining the CARSEL structure with the variables of finance, management, and internal auditing. The Back-Propagation Network (BNP) method is utilized for empirical estimation. The estimated results indicate that the execution of internal auditing in CDFAs has impact on their operating performance. The important factors affecting the performance of CDFAs in urban area are the auditing on loans, the delinquency of nonperforming loans, and the ratio of operating expenses over revenues. For CDFAs in rural area, the influencing factors are the auditing on loans and receipts, the ratio of operating expenses over revenues, and the ratio of nonperforming loans over net worth. However, the auditing on loans, the delinquency of nonperforming loans, the ratio of operating expenses over revenues, and the ratio of nonperforming loans over net worth, all have significant effects the performance of CDFAs in both urban and rural area. The implication of the research results shows that the execution of auditing is helpful for the performance of CDFAs in Taiwan.