The present invention provides a method for calibrating the crystal-level detection efficiency, which is capable of evaluating the influences caused by the penetration effect of the crystals of a scintillation detector so as to calculate the difference of detection efficiency between crystals correctly and thereby calibrate the difference between crystals appropriately such that the quality of the imaging result is improved accordingly. The method of present invention is simple without modifying the hardware design and consequently the design cost, manpower cost and time cost can be reduced.