Aiming at the problems of low image brightness, poor contrast, and blurred edges caused by insufficient illumination and noise during low-level-light imaging for multi-pixel photon counter (MPPC), an adaptive low-level-light image processing algorithm based on sub-window box filtering was proposed. To reduce the algorithm running time while highlighting the edge detail information of the image, the sub-window box filter was used to layer the image to obtain the basic layer and detail layer. For the image of basic layer, the adaptive threshold histogram equalization was used to stretch the contrast, and the image of detail layer was enhanced by adaptive gain control method. The fusion coefficient was determined adaptively based on the ratio of the number of effective gray values to the total gray in the image of basic layer, and the image of basic layer was fused with the image of detail layer to obtain the enhanced image. Three sets of low-level-light environments with different illumination levels were set by the low-level-light experimental platform for experimental simulation, which verified that the algorithm obtained better results in maintaining edge information and enhancing details. Experimental results show that the proposed algorithm is superior to the previous algorithm in objective evaluation of standard deviation, information entropy, and average gradient, which improves the imaging effect of low-level-light image.