The invention discloses a quick and precise high-throughput drug screening system based on deep learning. The drug screening system comprises a picture preprocessing module and a neural network module, wherein the picture preprocessing module comprises a channel merging module and a picture standardization module; the channel merging module merges different cell single-color channel pictures intothe multi-channel picture representation, wherein the merged picture tensors are represented as [H,W,C]; the picture standardization module standardizes the input multi-channel picture data into the tensor representation of [70,70,C]; the neural network module is connected with the picture standardization module, the input data of the neural network module is standardized picture tensors, and finally the trained neural network is subjected to final prediction classification prediction. The drug screening system DeepScreen based on deep learning has the advantages of being high in throughput, precise, efficient, fast, convenient, low in cost and resistant to interference, and has a worth-concerning practical and application prospect.