Eye movements are known to be well-quantitative indices to analyze a variety of neurological deficits as well as mechanisms for controlling motor systems both in scientific and clinical researches. In this study, a novel method we developed to measure the eye movement in mice, using bioadhesive polymer-coated phosphorescent particles, was applied for the calibration of the conventional video-oculography that tracks the pupil. We tested the vestibulo-ocular reflex, a reflexive eye movement observed across various species, and compared the values measured by the new method with ones measured by the conventional video-oculography. We found the difference between them was significant when the size of the pupil became small whereas those values were similar when the size of the pupil was relatively large. Our results suggest that there is a calibration factor related to the size of the pupil to improve the accuracy of the video-oculography and a potential benefit of our novel method to measure eye movements in rodents.