To address the microbial contamination of civil aircraft fuel tanks, the common microorganisms in the fuel tanks were classified. The growth condition and the growth mechanisms of microbial contamination in the civil aircraft fuel tanks were studied. The impact on the function, performance and safety of the aircraft structure, the fuel system and the power plant system were analyzed. For aircraft development and production stage, the microbial contamination protection design requirements of microorganisms were summarized in terms of the structural design of the fuel tanks and the design of the fuel system. For aircraft operation and storage stage, the prevention and monitoring measures requirements of microorganisms were put forward for service and maintenance. The preventive design and continuous monitoring of microorganisms during the life cycle of civil aircraft will effectively improve the ability of civil aircraft fuel tanks to prevent microbial contamination.