This study uses Grey System theory to analyze the accidents / incidents of F-104 jet fighters during their service period in Taiwan. The analysis classifies the F-104 jet fighter mishap records by Content Analysis into machine failure and six major human error types, including skill-based, rule-based, knowledge-based, communication-based, judgment-based and leadership-based. This study evaluates the nature of human error and understands potential elements that can harm pilots, crew and aviation organizations. The constrains of data quantity and the uncertainty of mishap level distribution mean that the traditional statistical methods cannot effectively handle the variables and relationships among the variables. Thus, the relational analysis of Grey System, which does not need large data bases and specific distribution patterns, has been used to address the factors that influence the aviation safety. The results reveal that the skill-based level has the most detrimental effect on the aviation of F-104, while machine failure also shows a strong effect. Suggestions are also discussed for the prevention of these factors in order to improve aviation safety.