The disclosure relates to a rapid and high precision centroiding method for spots image comprising the following steps. First, the method requires convoluting the gray value of a pixel with a Gaussian filter and judging whether the result thereof exceeds a predetermined threshold. If the value exceeds the predetermined threshold, the method requires marking the current pixel with a flag to identify which spot it belongs to, and then accumulating the product of the gray value and a coordinate value of the same spot; and at the same time, accumulating the gray value of the same spot; and saving the results of the accumulation respectively. If the gray value of the pixel does not exceed the predetermined threshold, the method requires marking the current pixel as a background flag. After all pixels of the image has been disposed of completely, the method includes calculating a quotient of the accumulations of the product of the gray value and the coordinate value and the accumulations of the gray value, and outputting the quotients. At the same time, a centroiding system for spots image is also presented.