In order to address the reliability allocation problem of the series system, a comprehensive reliability allocation method based on a transformed function of the failure mode and effects analysis is introduced. First, considering multiple factors that affect the reliability allocation, an allocation matrix is established by employing significance factors. Subsequently, to overcome the limitations of the conventional failure mode and effects analysis–based allocation method, non-linear transform laws of failure severity and occurrence, known as transformed functions, are established. The reliability allocation results could be adjusted appropriately by choosing transform coefficients according to the desired allocation results of the system. Then, the transformed failure mode and effects analysis and the comprehensive allocation matrix are combined to give an allocation vector. Finally, a computerized numerical controlled lathe and a spindle system are used as examples. The allocation results of the transformed method, the conventional failure mode and effects analysis method and those in the correlated references are compared to emphasize the significance of the proposed allocation method in engineering practice.