One of the most significant challenges in the application of brain-computer interfaces is the large performance variation, which often occurs over time or across users. Recent evidence suggests that the physiological states may explain this performance variation in BCI, however, the underlying neurophysiological mechanism is unclear. In this study, we conducted a seven-session motor-imagery experiment on 20 healthy subjects to investigate the neurophysiological mechanism on the performance variation. The classification accuracy was calculated offline by common spatial pattern and support vector (...) machine algorithms to measure the MI performance of each subject and session. Relative Power values from different rhythms and task stages were used to reflect the physiological states and their correlation with the BCI performance was investigated. Results showed that the alpha band RP from the supplementary motor area within a few seconds before MI was positively correlated with performance. Besides, the changes of RP between task and pre-task stage from theta, alpha, and gamma band were also found to be correlated with performance both across time and subjects. These findings reveal a neurophysiological manifestation of the performance variations, and would further provide a way to improve the BCI performance. (shrink)