The cyclopean eye serves as the reference point for determining visual direction in humans. Traditional theory places this point at the midpoint between the two eyes. However, this assumption overlooks individual differences in cyclopean eye positions, potentially leading to inconsistencies in viewing and interaction experiences within stereoscopic environments. Such discrepancies can notably reduce user interaction quality with stereoscopic display content, potentially hindering broader adoption of this technology. To address these differences, a method is developed for measuring cyclopean eye position coordinates using a stereoscopic display system. This technique involves incorporating a cyclopean eye testing experiment based on an improved average error method. Through subjective experimental measurements, we calculate the cyclopean eye positions of different users. The experimental results confirm that the proposed method effectively captures deviations in users' cyclopean eye position. Our findings are expected to develop strategies to improve interactive virtual reality experiences.