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The objective of pilot training is to equip trainees with the knowledge, judgment, and skills to maintain control of an aircraft and respond to critical flight tasks. The present research aims to investigate changes in trainees' cognitive control levels during a pilot training process while they underwent basic flight maneuvers. EEG microstate analysis was applied together with spectral power features to quantitatively monitor trainees' cognitive control under varied flight tasks during different training sessions on a flight simulator. Not only could EEG data provide an objective measure of cognitive control to complement the current subjective assessments, but the application of EEG microstate analysis is particularly well-suited for capturing rapid dynamic changes in cognitive states that may happen under complex human activities in conducting flight maneuvers. Comparisons were conducted between two types of tasks and across different training stages to monitor how pilot trainees' cognitive control responds to varied flight task types and training stages. The present research provides insights into the changes in trainees' cognitive control during a pilot training process and highlights the potential of EEG microstate analysis for monitoring cognitive control.