Covert channel is a way to building confidential channels based on the legitimate channels (also named with ‘overt channel’). Compared with the encryption technology, covert channel has stronger covertness because it conceals the behavior of covert communication as well as the transmitted message it contains. The emergence of covert channels has threatened the information security and personal privacy in public Internet. Some hackers and criminals, in particular, adopt covert channels to steal secret information bypassing the inspection of security facilities. It is, therefore, crucial to design and deploy more efficient and accurate detection algorithm for covert channels. In this study, a detection algorithm is proposed for covert timing channels based on the difference entropy. First, the definition of difference entropy is introduced, then, the principle of the algorithm is proposed, and the description of the implementation of this algorithm and parameter optimization is given. Lastly, the performance of the detection algorithm is evaluated through experiments, and experimental results show that proposed algorithm is effective on the detection of the IPCTC, TRCTC, JitterBug covert timing channels.