The invention relates to the technical field of cell counting and acquisition, in particular to a corneal endothelial cell counter positioning and photographing method based on iris characteristics, which comprises the following steps: S1, acquiring an image: observing a dynamic image of a detected eye window of a patient, aligning and focusing to reach an optimal state, and clicking a photographing button to finish image acquisition; and S2, image processing: S201, performing Gaussian smoothing on the image, performing gray processing on the image, and converting the generated gray image intoa binary image. According to the invention, gray scale change, de-noising, binarization change and morphological change are carried out on the cell image, subjective factors in cell morphological observation are reduced, point locations are conveniently marked in the pattern, a color sensor is added to conveniently carry out vertical comparison on the sampled image, a first marked point locationis conveniently found in N different front and back photos, and therefore, cell sampling can be carried out on the overlapped position.