Focal spot (light spot) at single-photon level have important applications in many fields. This report demonstrates a method for measuring focal spot size at the single-photon level indirectly. This method utilizes Silicon Photomultiplier (SiPM) as the single-photon sensitive detectors, combined with a nano-positioning stage. The approach involves one- or two-dimensional space scanning and a deconvolution operation, which enable evaluations of the size and spatial distribution of the focal spot formed by a single-photon-level pulsed laser. The results indicate that the average full width at half maximum of the focal spot is about 0.657 μm, which is close to the nominal resolution of the objective lens of the microscope (i.e. 0.42 μm). The proposed method has two key advantages: (1) it can measure focal spot at the single-photon level, and (2) the focal spot can easily be aligned with the detector because the array area of the Geiger mode avalanche photodiode (Gm-APD) cells in SiPM is usually on the order of square millimeter, and there is no need to put an optical slit, knife edge, or pinhole in front of the detector. The method described herein is applicable in weak focal spot detection related fields.