To solve the high storage cost and low retrieval speed problems in malicious Structure Query Language (SQL) detection faced by Nearest Neighbor (NN) method, a Hash learning based Malicious SQL Detection (HMSD) method was proposed. In this algorithm, Hash learning was used to learn the binary coding representation for SQL statements. Firstly, the SQL statements were presented as real-valued features by washing and deleting the duplicated SQL statements. Secondly, the isotropic hashing was used to learn the binary coding representation for SQL statements. Lastly, the retrieval procedure was performed and the detection speed was improved by using binary coding representation. Experimental results show that on the malicious SQL detection dataset Wafamole, the dataset is randomly divided so that the training set contains 10 000 SQL statements and the test set contains 30 000 SQL statements, at the length of 128 bits, compared with nearest neighbor method, the proposed algorithm has the detection accuracy increased by 1.3%, the False Positive Rate (FPR) reduced by 0.19%,the False Negative Rate (FNR) decreased by 2.41%, the retrieval time reduced by 94%, the storage cost dropped by 97.5%; compared with support vector machine method, the proposed algorithm has the detection accuracy increased by 0.17%, which demonstrate that the proposed algorithm can solve the problems of nearest neighbor method in malicious SQL detection.