The centroid estimation of the beacon spot is crucial to the pointing, acquisition, and tracking subsystem in inter-satellite optical wireless communication (IsOWC), especially for the received very weak beacon caused by a long link distance. In this work, we propose an accurate centroid positioning method to calculate the centroid of such a weak beacon with a low peak signal-to-noise ratio. The proposed method is based on the idea that uses the normalized amplitude of the gray gradient to enhance the weights near the center of the beacon spot. Both comparative numerical simulation and experimental verification are implemented, which demonstrate the effectiveness and feasibility of the proposed method. Compared to the gray centroid method, interpolation-based method, Hough transform method, and Gaussian fitting method, the proposed method has stronger robustness and higher accuracy, which could be helpful to applications in IsOWC as well as beacon-based pointing and tracking systems.