Objectives: Craft unions typically collect the national health insurance premiums from all members at one time and then pay the premiums in instalments. However, this method involves a high risk that the premiums have been collected but not paid. This study identified the key factors for financial anomalies and proposed suggestions for craft unions regarding financial anomaly management mechanisms. Methods: Combining qualitative and quantitative methods, this study conducted onsite interviews on the personnel of the Bureau of Labor Insurance and performed questionnaire survey on the personnel of government authorities on labor affairs as well as 303 craft unions that participated in the national insurance program in Taichung, Changhua, and Nantou, Taiwan. Moreover, data mining and statistical analysis were performed on the actual data missing in the financial inspection on craft unions’ health insurance premiums and the unions’ overdue payment records from 2012 to 2016. Finally, triangulation was conducted for data cross-validation. Results: The Bureau of Labor Insurance facilitated financial monitoring on craft unions by imposing the penalty of terminating grant disbursement. In addition, 85% of the financial audit items used by the unions were consistent with that adopted by the National Health Insurance Administration. Government authorities on labor affairs in Taichung, Changhua, and Nantou were willing to collaborate with health insurance authorities for the management of craft unions with financial anomalies. Moreover, 24% of the craft unions showed insufficient internal control and lacked a financial management mechanism; 87.6% of the union members supported external financial audit and suggested strictly examining whether the insurance premiums were misappropriated. Through onsite interview, questionnaire survey, chi-square analysis, and logistic regression analysis, four key factors for financial anomalies (overdue bills) among craft unions were determined, namely “no exclusive account established for health insurance premiums”, “misappropriation of the premiums saved in the exclusive account”, “the exclusive account for health insurance premiums not opened and managed by more than two people”, and “insufficient balance of the health insurance premium deposit”. Conclusions: The items used in the craft union financial audit that are commonly adopted by the National Health Insurance Administration, Bureau of Labor Insurance, and county and city governments can be used as the basis for collective financial monitoring across agencies. This study combined four key factors for financial anomalies with the current 27 items used in the financial inspections on craft unions’ health insurance premiums and divided the level of influence of missing inspection data into strong, moderate, and weak. Finally, this study constructed a health insurance financial anomaly classification management model for craft unions and proposed concrete suggestions according to the research results and the current work status of the Central Division of the National Health Insurance Administration.