Cognitive control is adaptive in that it rapidly adjusts attention in response to changing contexts and shifting goals. Research provides evidence that cognitive control can rapidly adjust attention to focus on task-relevant information based on prior conflict experience. Neural encoding of goal-related information is critical for goal-directed behaviour; however, the empirical evidence on how conflict experience affects the encoding of cognitive conflict in the brain is rather weak. In the present fMRI study, a Stroop task with different proportions of incongruent trial was used to investigate the neural encoding of cognitive conflict in the environment with changing conflict experience. The results showed that the anterior cingulate cortex, dorsolateral prefrontal cortex, and intraparietal sulcus played a pivotal role in the neural encoding of cognitive conflict. The classification in anterior cingulate cortex was significantly above chance in the high-proportion, moderate-proportion, and low-proportion conflict conditions conducted separately, suggesting that neural encoding of cognitive conflict in this region was not altered based on proportion of conflict. The dorsolateral prefrontal cortex and intraparietal sulcus showed significant above-chance classification in the moderate-proportion and low-proportion conflict conditions, but not in the high-proportion conflict condition. These findings provide direct evidence that conflict experience modulates the neural encoding of cognitive conflict.