In the face of the increasing complexity of risk factors in the coal mining transportation system (CMTS) during the process of intelligent transformation, this study proposes a method for analyzing accidents in CMTS based on fault tree analysis (FTA) combined with Bayesian networks (BN) and preliminary hazard analysis (PHA). Firstly, the fault tree model of CMTS was transformed into a risk Bayesian network, and the inference results of the fault tree and Bayesian network were integrated to identify the key risk factors in the transportation system. Subsequently, based on the preliminary hazard analysis of these key risk factors, corresponding rectification measures and a risk control system construction plan are proposed. Finally, a case study was carried out on the X coal mine as a pilot mine to verify the feasibility of the method. The application of this method effectively identifies and evaluates potential risk factors in CMTS, providing a scientific basis for accident prevention. This research holds significant importance for the safety management and decision making of coal mine enterprises during the process of intelligent transformation and is expected to provide strong support for enhancing the safety and reliability of CMTS.