The invention discloses a centering method of a spiral scanning type surface topography measuring system. The method is characterized by comprising the steps of fixing a centering testing member on aZ-direction rotating platform, wherein the lower surface of the centering testing member is a horizontal surface, and the upper surface is an oblique surface, then rotating the Z-direction rotating platform by one circle, measuring a height difference deltah of the movement track of a probe relative to the upper surface of the centering testing member by a measuring head, then making an X-direction linear platform move along an X-direction by a small distance deltax', then making a Z-direction rotating platform by one circle, and measuring a height difference deltah' of the movement track of the probe relative to the upper surface of the centering testing member by the measuring head; introducing the two height differences which are measured in the two times into a relational expression, and obtaining an X-direction centering error deltax and a Y-direction centering error deltay between a scanning starting point of a measuring head probe and the rotating center of a Z-direction rotating platform. The centering method has advantages of high centering operation, high centering speed, high centering precision and high resolution.