Considering the characteristic of Logistic chaos system varying with the parameter μ, and the feature that the multiscale entropy reflects the degree away from the equilibrium, a new method is proposed to estimate the characteristic of Logistic nonlinear system based on multiscale entropy. Numerical simulations prove that different states of Logistic chaos system can be distinguished based on multiscale entropy, and quantifiable nonlinear dynamical behavior index is obtained. This work provides a theoretical basis for understanding Logistic chaos analysis and chaos application of secret communication.