Intelligent methods have long been researched in fault diagnosis. Traditionally, feature extraction and fault classification are separated, and this process is not completely intelligent. In addition, most traditional intelligent methods use an individual model, which cannot extract the discriminate features when the machines work in a complex condition. To overcome the shortcomings of traditional intelligent fault diagnosis methods, in this paper, an intelligent bearing fault diagnosis method based on ensemble sparse auto-encoders was proposed. Three different sparse auto-encoders were used as the main architecture. To improve the robustness and stability, a novel weight strategy based on distance metric and standard deviation metric was employed to assign the weights of three sparse auto-encodes. Softmax classifier is used to classify the fault types of integrated features. The effectiveness of the proposed method is validated with extensive experiments, and comparisons with the related methods and researches on the widely-used motor bearing dataset verify the superiority of the proposed method. The results show that the testing accuracy and the standard deviation are 99.71% and 0.05%.