Subjectively reported sleepiness and objectively measured vigilance are often used to assess and monitor operating performance. Evidence suggests that the response patterns of the two measures are independent of each other. However, the neural mechanism underlying this phenomenon remains unclear. This study aimed to investigate whether subjective sleepiness and objective vigilance were associated with each other. Thirty-three participants were subjected to 34 h of acute sleep deprivation. We collected sleepiness, vigilance, and resting-state fMRI data. We also located the neural mechanism of isolation of object and subject parameters. Firstly, the correlation analysis showed that there was no statistically significant correlation between the changes in vigilance and sleepiness during the sleep deprivation period. Then, implementing the support vector machine algorithm through functional connectivities as features, we found that different functional connectivity patterns underline the isolation of these two factors during sleep deprivation. The functional connectivities involved in characterizing the vulnerability of objective vigilance are more extensive, involving the connectivities within the sensorimotor network, between the subcortical and cortical network, and among multiple cortical networks. The functional connectivity involved in characterizing the vulnerability of subjective sleepiness is limited to the communication between the subcortical thalamus and the somatosensory cortex. In addition, we found that implementing global signal regression would reduce the model's power to predict vigilance and sleepiness. This work contributes to our understanding of how sleep deprivation affects individual cognition and behavior, and will be of use in the evaluation and prediction of cognitive performance during sleep loss. The online version contains supplementary material available at 10.1007/s11571-021-09772-0.