With the increasing population of Industry 4.0, industrial big data (IBD) has become a hotly discussed topic in digital and intelligent industry field. The security problem existing in the signal processing on large scale of data stream is still a challenge issue in industrial internet of things, especially when dealing with the high-dimensional anomaly detection for intelligent industrial application. In this article, to mitigate the inconsistency between dimensionality reduction and feature retention in imbalanced IBD, we propose a variational long short-term memory (VLSTM) learning model for intelligent anomaly detection based on reconstructed feature representation. An encoder-decoder neural network associated with a variational reparameterization scheme is designed to learn the low-dimensional feature representation from high-dimensional raw data. Three loss functions are defined and quantified to constrain the reconstructed hidden variable into a more explicit and meaningful form. A lightweight estimation network is then fed with the refined feature representation to identify anomalies in IBD. Experiments using a public IBD dataset named UNSW-NB15 demonstrate that the proposed VLSTM model can efficiently cope with imbalance and high-dimensional issues, and significantly improve the accuracy and reduce the false rate in anomaly detection for IBD according to F1, area under curve (AUC), and false alarm rate (FAR).