This paper analyzes the influence of parameters’ uncertainty on the system response. The stochastic uncertainty, cognitive uncertainty, and stochastic-cognitive mixed uncertainty are discussed based on a double link flexible joint manipulator. The conclusions are achieved by comparing the distance between the upper and lower boundaries of the 95% confidence regions of the response and between each group of confidence region. The probability theory and interval method are used to deal with the random and cognitive uncertainty of parameters, and the mixed uncertainty of parameters is treated with the improved double-loop Monte-Carlo method. The simulation results show that the analysis of the mixed uncertainty of parameters is expected to concretely represent the impact of uncertainty on the system response. In addition, the uncertainty analysis method provides a theoretical basis for analyzing the sensitivity of the parameters in the time domain.