The invention relates to a method and a system for measuring geometric error of a machine tool based on a one-dimensional measuring head and standard balls. The method comprises the following steps ofS1, according to the type of a numerically-controlled machine tool, arranging the standard balls at multiple position points on the numerically-controlled machine tool, and utilizing the one-dimensional measuring head in the vertical direction to measure the three-dimensional offset of the center of each standard ball on the numerically-controlled machine tool; S2, on the basis of a geometric error model of the numerically-controlled machine tool, obtaining the position-related geometric error of the numerically-controlled machine tool according to the obtained three-dimensional offset of thecenter of each standard ball at each position point in S1. Compared with the prior art, the method has the advantages that the eccentricity of the center of each standard ball due to the geometric error of the machine tool is measured by the one-dimensional measuring head, the measuring value is used as coordinate reference, and the problem of failure of the machine-mounted measuring head due todegrading of the accuracy of the machine tool is effectively solved; the geometric constraint on the measuring head in the measuring process is avoided, the difficulty in numerical control programmingof the movement track of the measuring head is effectively decreased, and the damage risk of the measuring system due to mistake of the movement track is eliminated.