With the advancement of data science, the collection of increasingly complex datasets has become commonplace. In such datasets, the data dimension can be extremely high, and the underlying data generation process can be unknown and highly nonlinear. As a result, the task of making causal inference with high-dimensional complex data has become a fundamental problem in many disciplines, such as medicine, econometrics, and social science. However, the existing methods for causal inference are frequently developed under the assumption that the data dimension is low or that the underlying data generation process is linear or approximately linear. To address these challenges, this paper proposes a novel stochastic deep learning approach for conducting causal inference with high-dimensional complex data. The proposed approach is based on some deep learning techniques, including sparse deep learning theory and stochastic neural networks, that have been developed in recent literature. By using these techniques, the proposed approach can address both the high dimensionality and unknown data generation process in a coherent way. Furthermore, the proposed approach can also be used when missing values are present in the datasets. Extensive numerical studies indicate that the proposed approach outperforms existing ones.