The present invention provides a technique for eliminating the effect of the thermal drift and other variances and to improve the observing or manipulating accuracy of a scanning probe microscope or atom manipulator by using the technique to correct the aforementioned change in the relative position of the probe and the sample due to heat or other factors during the observation or manipulation. To obtain an image of the sample surface at the atomic level or perform a certain manipulation on an atom on the sample surface, the present invention can be applied to a probe position control method for controlling the relative position of the probe and the sample while measuring an interaction between the objective atom on the sample surface and the tip of the probe. In the present method, the relative position of the probe and the sample are changed while the probe is oscillated relative to the sample in two directions parallel to the sample surface at frequencies of f1 and f2 (S1a). Meanwhile, a point (or characteristic point) where the frequencies f1 and f2 disappear from the measured value of the interaction working in the direction perpendicular to the sample surface is detected (S1b). Then, the relative movement of the probe and the sample is controlled so that the measurement value thereby detected is maintained (i.e. the characteristic point is tracked; S1c), and the speed of the aforementioned relative movement is determined (S1d). Subsequently, the relative position control is corrected using the detected speed (S2).