Transmission efficiency is one of the key performance parameters of the harmonic drive. Hence, it is significant to calculate its transmission efficiency accurately and conduct reliability analysis under different operation conditions of the harmonic drive. In this paper, based on the principles of reliability science and the belief reliability theory, the belief reliability modeling and analysis for the transmission efficiency of the harmonic drive is proposed. First, considering the power loss during the transmission of harmonic gears, the theoretical model for the transmission efficiency of harmonic gears is constructed, where the multiple external factors that affect the transmission efficiency, including lubrication methods, load torque, rotating, and environmental temperature are considered by introducing an agent model. The transmission efficiency margin model is constructed by calculating the distance between the transmission efficiency and its threshold. Then, the uncertainty analysis and quantification are conducted and the belief reliability model for the transmission efficiency of the harmonic drive is constructed, where the probability measure is employed to describe aleatory uncertainties. After that, the unknown parameters in the transmission efficiency model are estimated through maximum likelihood estimation method using transmission efficiency testing data to achieve the combination of the theoretical model and testing data. Finally, a case study of XB40-100 harmonic reducer is used to illustrate the practicability and efficiency of the proposed method. The results show that the proposed method can combine the testing data with the theoretical model effectively and calculate the transmission efficiency of the harmonic reducer accurately under the given lubrication method, load, rotating speed, and temperature conditions. The belief reliability analysis results reveal that it is conducive to improve the transmission efficiency margin and its belief reliability by increasing the load torque, reducing the rotating speed, or increasing the environmental temperature appropriately.