The invention belongs to the technical field of measurement for diagnostic purposes and discloses a fluorescent target reconstruction result post-processing method based on three-way decision. The method comprises the following steps: dividing a target into three parts, namely a target area, a boundary area and a background area according to a global reconstruction result by utilizing a three-waydecision theory; merging the target area and the boundary area, forming a target feasible area, and reconstructing in the area again; performing post-processing on the reconstruction effect in the feasible area, and dividing the target area, the boundary area and the background area, wherein the target area is the final result. According to the method disclosed by the invention, a target feasiblearea extraction method is obtained according to the three-way decision theory, the reconstruction problem ill-posed property is effectively reduced, and the solution stability and reconstruction result are improved. The final reconstruction result shows that a position error is 1.03mm, and the reconstruction accuracy is obviously improved. The reconstruction result is post-processed according to the three-way decision theory, the target area, the boundary area and the background area are clearly obtained, and huge convenience is provided.