A high-throughput virtual drug screening system based on molecular fingerprints and deep learning, includes a deep-learning model online-modeling subsystem and an online virtual-screening subsystem. The system combines the molecular fingerprints and a deep neural network method to construct a high-throughput virtual drug screening system. The system includes built-in structural-diversity screening libraries and realizes the online automatic construction of deep learning models and virtual screening. The system helps researchers in the drug discovery industry such as medicinal chemistry to conduct rapid screening through their desired targets to obtain potential active compounds and accelerate drug discovery.