A calibration method for deposition rates of multilayer coatings by sputtering depositions was proposed to eliminate the random thickness errors and to realize the accurate control of film thicknesses. In this method,the deposition rates were acquired by the least square fitting for results of different deposition experiments. An analysis on the basic properties of random variables shows that deposition rates can be converged to the true values in a case that the number of depositions is large enough. On the basis of above principle, accurate deposition rates can be acquired, random thickness errors can be extracted, and the thickness control accuracy of the coating machine can be determined as well. Furthermore, the complete information to realize the accurate control of film thicknesses can be also obtained. Experiments based on this calibration method were carried out by using two deposition systems. Results indicate that control accuracies are different for different deposition systems. The low cost deposition system shows a relative low thickness control accuracy in 0.1 nm,and the other one with high deposition performance could realize the thickness control accuracy in 0.01 nm.