Automatic detection of apple defects using a computer vision system is difficult due to the similarity between stem-end/calyx and true defects. Identification of stem-end/calyx is always a challenging project in automatic apple grading. This paper presents an encoding method based on position change for spot-array structured light, and the proposed method was used in distinguishing defects from stem-end/calyx of apple images in real time. By analyzing imaging process of the spots projected onto the object surface and reference plane, the position change of spot was chosen as coded primitive. Over the field of two elements, the M-array was generated by using the primitives, and was used as the coded pattern of near-infrared(NIR) spot-array structured light. Analysis of difference matrix made it possible to identify the location of stem-end/calyx regions after matching. The on-line experimental results demonstrated that the proposed method could realize the detection of stem-end/calyx efficiently, and achieve an average of 93.17％ recognition accuracy with real-time performance. The results indicated that the proposed method was effective in identification of apple stem-end/calyx.