A hydraulic system is a key subsystem of heavy-duty machine tools with a high failure intensity, the failure of which often causes shutdown of production and economic loss in machining. Therefore, it is necessary to implement failure analysis to identify the weak links of system and improve the reliability. For hydraulic system, there is often an amount of failure data collected in field, which help to calculate the occurrence probability of basic events through fault tree analysis method. However, the data are incomplete and uncertain. To address this issue, this study presents a fault tree analysis methodology. Experts’ opinions are utilized, combined with field data based on the Dempster–Shafer theory and rough set theory to fill the incompleteness and eliminate the uncertainty. For application in a case study, a fault tree of the hydraulic system of heavy-duty machine tools is firstly constructed. Then, the importance analysis is performed to help identify the weak links of hydraulic system. The results show the critical basic events affecting the safety and reliability of a hydraulic system.