Pilot factor is worth considering when analyzing the causes of civil aviation accidents. This study introduces a data-driven Bayesian network (BN) approach to investigating the joint causal effects of pilot and other factors on civil aviation safety. A total number of 163 individual pilot-related accidents in the National Transportation Safety Board (NTSB) aviation accident database from 2008 to 2020 are analyzed, focusing on eliciting the causal effects of various potential risk factors, including pilot factors, on civil aviation accidents. The modeling of the interdependency among the risk influencing factors (RIFs) and their causal contributory effect on the accident outcome is structured by a tree augmented network (TAN) and validated by sensitivity analysis. The novelty of this study is to incorporate pilot factors derived from the civil aviation accident database into risk analysis, combined with other external factors. The results indicate that weather conditions and flight phases are more correlated with casualty types of civil aviation accidents than pilot action and decision, and three other pilot factors only contribute to fatal injury in civil aviation accidents.