In order to make the results more accurate, based on the above findings obtained from single-factor experiments, orthogonal experiments are conducted, since there are impacts of interactions between many factors. It is noted that four factors, milling rotational speed, RGM, ball type and pH value, have great influences on CIP degradation efficiency, and the results of orthogonal experiments involving these four factors are displayed in Table 3. It can be seen that a highest degradation efficiency of 95.846% is achieved when the milling rotational speed is 300 rpm, RGM is 3:1, grinding media is steel ball, and pH value is 5. As for range analysis (parameter R), the R value is 35.484, 10.191, 29.928, and 26.917, corresponding to factor A, B, C and D, respectively. Therefore, factor A (milling rotational speed) affects CIP degradation efficiency most in MCT process, and factor B (RGM) has less influence on that, while factors C and D have significant influence on that. In addition, through the mean analysis (K1, K2 and K3 values), we can conclude that the optimum combination is A1B3C1D1, that is, the milling rotational speed is 300 rpm, RGM is 5:1, grinding media is steel ball, and pH value is 5. In short, the orthogonal experiments can help us look for the main influencing factors, and guide the CIP remediation work in the real world.