With the advantage of in situ measurement, the three-probe method is commonly used to measure either the error motion of high-precision spindles or the roundness error of artifacts. The roundness error of artifacts or spindle errors can be obtained through solving error-separation equations. Both the time- and frequency-domain solutions of the three-probe method are presented. In addition, the key points of solutions, i.e., the rounding error induced by inconsistency of sampling points, harmonic suppression, and averaging schemes of multiple revolutions into one circle, are described in detail. Experiments were conducted to compare the two solutions and quantify the influence of setup parameters, including rotational speed probe arrangement, consistency of sampling points, and number of revolutions. The results showed that the roundness error of the time-domain solution was inaccurate due to large rounding errors, while that of the frequency-domain solution with the previous average scheme was accurate. In contrast, the spindle error of the frequency-domain solution with the latter average scheme was more reliable. The findings provided a reference to recommend setup parameters depending on the aim of the three-probe method.