Dimensional deviation is a prerequisite for improving the manufacturing process of parts with free-form surfaces, for example, the reverse adjustment of the die cavity of turbine blade. Influenced by random noise of the manufacturing process, dimensional variation is inevitable for batch parts. Therefore, it may cause unacceptable error to estimate batch parts dimensional deviation by a single sample. Meanwhile, the optimum sample size for estimating dimensional deviation is difficult to determine. To overcome this problem, a practical method for estimating of dimensional deviation of parts with free-form surface is proposed. Firstly, displacements of the discrete points on part surface are employed to represent dimensional error of the part. Estimating dimensional deviation of parts is actually to estimate the simultaneous confidence intervals of the discrete point displacements. Secondly, Bonferroni simultaneous confidence intervals are adopted to estimate the confidence intervals of the part dimensional deviation. Moreover, the accuracy of the estimation will be continuously improved by increasing samples. Consequently, a practical dimensional deviation estimation method is presented. Finally, a compressor blade is adopted to illustrate the proposed method. The percentage of estimation error of the blade dimensional deviation that is less than 0.05mm, which is the estimation error limit, of all the 100 times sampling experiments is 99%, exceeding the given confidence level of 95%, while the percentage of the existing method is below the confidence level, only 87%.