Reservoir models are generated by geostatistics using available static data. However, there is inherent uncertainty in the reservoir models due to limited information. A number of reservoir models with equivalent probabilities are created to quantitatively assess model uncertainty. The easiest way to evaluate the uncertainty is to perform a reservoir simulation for hundreds of reservoir models, but the simulation cost is too high. Recently, distance-based clustering (DBC) has been used as a means of efficient uncertainty assessment. DBC classifies similar reservoir models into the same group. Because models belonging to the same group have similar reservoir performances, simulating a representative model for each group will give a comparable uncertainty range from simulating all models. For DBC to be successful, the definition of distance, which represents non-similarity between models, is the key factor.In this research, after the main information from a reservoir model is extracted through a stacked autoencoder (SAE), which is one of deep learning algorithms, the 2-norm of feature vectors for two models is defined as the distance. First, the hyperparameters for SAE are analyzed by sensitivity analysis in order to optimize the feature vector from reservoir facies model. Similar to other artificial neural network algorithms, uncertainty results are sensitive to the number of neurons and the number of hidden layers but are stable for the number of clusters. After SAE-based clustering, only 20 representative models can realize the uncertainty range present in 800 individual initial models. If there are observed dynamic data, the best representative model can be determined by a misfit between the simulated production from the representative models and the observed data. The best model and its 9 closest models in feature space are selected as qualified models from among the entire 800 models. Additional reservoir simulations for the closest models can dramatically improve the uncertainty range of the prior models without inverse algorithms. The 10 qualified models can be utilized for generating pseudo-static data or can be used as initial models for inverse algorithms for further improvement of reservoir characterization.