The covertness of an active sonar is a very important issue and the sonar signal waveform design was studied to improve covertness of the system. Click is one of the most common cetacean sounds, and has excellent detection performance. Meanwhile, existing interception systems normally classify cetacean sounds as ocean noise and filter them out. Based on this, a bio-inspired covert active sonar detection method is proposed by encoding the clicks produced by sperm whales. First, based on the frequency distribution characteristic of sperm whale clicks and frequency-hopping sequence, a set of bionic sub-pulses are constructed by encoding the centroid frequency of the real clicks. Based on the inter-click interval characteristic of the clicks and time-hopping sequence, the bionic sonar signal is constructed by combining the constructed bionic sub-pulses and encoding the inter-pulse interval between two adjacent pulses. Then, a single bionic sonar signal is utilized to estimate the speed and range of the target. Based on the characteristics of sperm whale click trains, a camouflage application method is designed to improve the camouflage ability of the bionic sonar signal. Finally, experiment results show that when the target speed is 5m/s and 10m/s and the signal to noise ratio varies from −20dB to 20dB, the root-mean-square error of estimated speed and range are lower than 0.1m/s and 0.1m, respectively. In addition, the constructed bionic sub-pulses have a 99% probability of being classified into sperm whale clicks. Experimental results demonstrate the effectiveness and covertness of the proposed method.