Subsea manifold system is a complex system that occupies a pivotal role in contemporary ocean engineering and has a significant impact on the safety of marine resource exploitation. Reliability technology plays a significant role in ensuring the safe operation of the subsea manifold system. To perform a comprehensive analysis of the reliability of complex systems, a combination method of FMECA-FFTA (Failure Modes, Effects and Criticality Analysis - Fuzzy Fault Tree Analysis) is introduced in this study. Firstly, FMECA is used to accomplish a qualitative analysis of system reliability considering multifactorial failure modes, which included analyzing potential failure modes, causes of system failure, and evaluating the degree of hazard to the system through a risk matrix diagram. Then, FFTA is applied to build a fault tree model to divide the system into “system-subsystem-component” and determine the minimal cut sets for quantitative analysis of system reliability. In addition, fuzzy set theory is incorporated to improve the accuracy of handling uncertainty in quantitative reliability analysis. Finally, a qualitative and quantitative reliability analysis is conducted by using FMECA-FFTA method for subsea manifold system. The failure modes of the subsea manifold system are clearly identified, including high-risk modes such as external leakage, medium-high-risk modes such as fail to close/lock on demand, and medium-risk modes such as leakage of critical location, plugged, and effective measures should be taken to focus on preventive protection and regular testing for the high risk, medium-high risk and medium risk modes.