Existing light pen systems are required to arrange a plurality of measuring spots to overcome the geometric constraints of a measuring terminal. This will result in a complicated measuring terminal structure. Moreover, it is disadvantageous to use the light pen system in limited measurement space. In this work, the light field imaging method is introduced into a light pen type measurement system. The epipolar plane image (EPI) of the light spot on the light pen is obtained using the light field imaging principle, and the spinning parallelogram operator (SPO) is adopted to calculate the slope of diagonal line on EPI. Subsequently, the depth information of the light-emitting point is estimated and the wrong solution of the PNP (perspective-n-points) algorithm is eliminated. Ultimately, accurate three-dimensional coordinate for the measured point are obtained. The effectiveness of the proposed method is verified by experiments. The proposed method only requires a monocular light field camera combined with three-point light pen to complete the measurement of three-dimensional coordinate value. Thus, the operation of the light pen measurement system can be greatly simplified.