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Objective: The aim of this study was to investigate the correlation between 3D visual fatigue and physiological measures by canonical correlation analysis enabling to categorical correlation. Background: Few studies have been conducted to investigate the physiological mechanism underlying the visual fatigue caused by processing 3D information which may make the cognitive mechanism overloaded. However, even the previous studies lack validation in terms of the correlation between physiological variables and the visual fatigue. Method: 9 Female and 6 male subjects with a mean age of 22.53±2.55 voluntarily participated in this experiment. All participants were asked to report how they felt about their health sate at after viewing 3D. In addition, Low & Hybrid measurement test(Event Related Potential, Steady-state Visual Evoked Potential)and for evaluating cognitive fatigue before and after viewing 3D were performed. The physiological signal were measured with subjective fatigue evaluation before and after in watching the 3D content. For this study suggesting categorical correlation,all measures were categorized into three sets such as included Visual Fatigue set(response time, subjective evaluation),Autonomic Nervous System set(PPG frequency, PPG amplitude, HF/LF ratio), Central Nervous System set(ERP amplitude P4, O1, O2, ERP latency P4, O1, O2, SSVEP S/N ratio P4, O1, O2). Then the correlation of three variables sets, canonical correlation analysis was conducted. Results: The results showed a significant correlation between visual fatigue and physiological measures. However, different variables of visual fatigue were highly correlated to respective HF/LF ratio and to ERP latency(O2). Conclusion: Response time was highly correlated to ERP latency(O2) while the subjective evaluation was to HF/LF ratio. Application: This study may provide the most significant variables for the quantitative evaluation of visual fatigue using HF/LF ratio and ERP latency based human performance and subjective fatigue.