In order to predict the geometric error of machine tool guide more accurately, a geometric error prediction method based on tolerance was designed, and the mapping relationship between surface topography error and geometric error was given. Sampling dual-frequency laser interferometer can realize the advantages of high precision, fast response and high resolution, which can fully meet the needs of high precision displacement testing. Thirty-seven measuring points were set for the travel of X-axis guide rail in an equidistance manner. After the sliding plate arrived at each measuring position and stayed for 6s to complete the sampling process, the R2 parameter of the fitting curve of the circular marking position could reach the ideal fitting accuracy. There is a difference of 0.15 μm between the actual measured data and the predicted results. Compared with the geometric error test results, most of the residuals are small, and the maximum residuals are controlled within 10% of the measured results. The proposed method can accurately predict the geometric error of the guide rail in the initial design process of the machine tool based on the tolerance. This study has a good theoretical significance for improving the accuracy of machine tools and is easy to be applied in practice.