Continuous task engagement generally leads to vigilance decrement and deteriorates task performance. However, how conflict effect is modulated by vigilance decrement has no consistent evidence, and little is known about the underlying neural mechanisms. Here we adopted an electroencephalogram dataset collected during a prolonged flanker task to examine the interactions between vigilance and congruency on behavioral performance and neural measures. Specifically, we extracted a sequence of ERPs using temporal principal component analysis (PCA) and performed functional network analysis with graph measures. Behavioral analysis results showed that behavioral performance deteriorated due to vigilance decrement, but the capability of conflict processing was maintained over time. Regarding the neural analysis results, the conflict effect reflected in P3a and P3b was changed and maintained respectively when affected by vigilance decrement. The theta band frontoparietal network was observed in the face of conflicting interference and the conflict effect for graph measures disappeared over time. These results demonstrated deteriorated task performance, impaired cognitive functions, and the reconfiguration of cognitive control networks during a prolonged flanker task. Our findings also support the evidence that temporal PCA and event-related network analysis might be efficient for the investigation of the neural dynamics of complex cognitive processes.