Missing values are ubiquitous in industrial data sets because of multisampling rates, sensor faults, and transmission failures. The incomplete data obstruct the effective use of data and degrade the performance of data-driven models. Numerous imputation algorithms have been proposed to deal with missing values, primarily based on supervised learning, that is, imputing the missing values by constructing a prediction model with the remaining complete data. They have limited performance when the amount of incomplete data is overwhelming. Moreover, many methods have not considered the autocorrelation of time-series data. Thus, an adaptive-learned median-filled deep autoencoder (AM-DAE) is proposed in this study, aiming to impute missing values of industrial time-series data in an unsupervised manner. It continuously replaces the missing values by the median of the input data and its reconstruction, which allows the imputation information to be transmitted with the training process. In addition, an adaptive learning strategy is adopted to guide the AM-DAE paying more attention to the reconstruction learning of nonmissing values or missing values in different iteration periods. Finally, two industrial examples are used to verify the superior performance of the proposed method compared with other advanced techniques.