In many important machine learning applications, the training distribution used to learn a probabilistic classifier differs from the distribution on which the classifier will be used to make predictions. Traditional methods correct the distribution shift by reweighting training data with the ratio of the density between test and training data. However, in many applications training takes place without prior knowledge of the testing distribution. Recently, methods have been proposed to address the shift by learning the underlying causal structure, but those methods rely on diversity arising from multiple training data sets, and they further have complexity limitations in high dimensions. In this paper, we propose a novel Deep Global Balancing Regression (DGBR) algorithm to jointly optimize a deep auto-encoder model for feature selection and a global balancing model for stable prediction across unknown environments. The global balancing model constructs balancing weights that facilitate estimation of partial effects of features (holding fixed all other features), a problem that is challenging in high dimensions, and thus helps to identify stable, causal relationships between features and outcomes. The deep auto-encoder model is designed to reduce the dimensionality of the feature space, thus making global balancing easier. We show, both theoretically and with empirical experiments, that our algorithm can make stable predictions across unknown environments. Our experiments on both synthetic and real datasets demonstrate that our algorithm outperforms the state-of-the-art methods for stable prediction across unknown environments.