With the development of deep learning (DL) techniques, rotating machinery intelligent diagnosis has gone through tremendous progress with verified success and the classification accuracies of many DL-based intelligent diagnosis algorithms are tending to 100\%. However, different datasets, configurations, and hyper-parameters are often recommended to be used in performance verification for different types of models, and few open source codes are made public for evaluation and comparisons. Therefore, unfair comparisons and ineffective improvement may exist in rotating machinery intelligent diagnosis, which limits the advancement of this field. To address these issues, we perform an extensive evaluation of four kinds of models, including multi-layer perception (MLP), auto-encoder (AE), convolutional neural network (CNN), and recurrent neural network (RNN), with various datasets to provide a benchmark study within the same framework. We first gather most of the publicly available datasets and give the complete benchmark study of DL-based intelligent algorithms under two data split strategies, five input formats, three normalization methods, and four augmentation methods. Second, we integrate the whole evaluation codes into a code library and release this code library to the public for better development of this field. Third, we use specific-designed cases to point out the existing issues, including class imbalance, generalization ability, interpretability, few-shot learning, and model selection. By these works, we release a unified code framework for comparing and testing models fairly and quickly, emphasize the importance of open source codes, provide the baseline accuracy (a lower bound) to avoid useless improvement, and discuss potential future directions in this field. The code library is available at https://github.com/ZhaoZhibin/DL-based-Intelligent-Diagnosis-Benchmark.