Preparatory brain activity is a cornerstone of proactive cognitive control, a top-down process optimizing attention, perception, and inhibition, fostering cognitive flexibility and adaptive attention control in the human brain. In this study, we proposed a neuroimaging-informed convolutional neural network model to predict cognitive control performance from the baseline pre-stimulus preparatory electrophysiological activity of core cognitive control regions. Particularly, combined with perturbation-based occlusion sensitivity analysis, we pinpointed regions with the most predictive preparatory activity for proactive cognitive control. We found that preparatory arrhythmic broadband neural dynamics in the right anterior insula, right precentral gyrus, and the right opercular part of inferior frontal gyrus (posterior ventrolateral prefrontal cortex), are highly predictive of prospective cognitive control performance. The pre-stimulus preparatory activity in these regions corresponds to readiness for conflict detection, inhibitory control, and overall elaborate attentional processing. We integrated the convolutional neural network with biologically inspired Jansen-Rit neural mass model to investigate neurostimulation effects on cognitive control. High-frequency stimulation (130 Hz) of the left anterior insula provides significant cognitive enhancement, especially in reducing conflict errors, despite the right anterior insula’s higher predictive value for prospective cognitive control performance. Thus, effective neurostimulation targets may differ from regions showing biomarker activity. Finally, we validated our theoretical finding by evaluating intrinsic neuromodulation through neurofeedback-guided volitional control in an independent dataset. We found that left anterior insula was intrinsically modulated in real-time by volitional control of emotional valence, but not arousal. Our findings further highlight central role of anterior insula in orchestrating proactive cognitive control processes, positioning it at the top of hierarchy for cognitive control.