We demonstrate a composite multiscale entropy (CMSE) method of terahertz (THz) signal complexity analysis to distinguish different biological tissues. The THz signals reflected from fresh porcine skin and muscle tissues were measured and analyzed. The statistically significant difference and separation of the two tissues based on several parameters were analyzed and compared for THz spectroscopy and imaging, which verified the better performance of the CMSE method and further enhancement of the contrast among THz signals that interact with different tissues. This process provides a better analysis and discrimination method for THz spectroscopy and imaging in biomedical applications.