The present study sought to investigate the neural basis of implicit learning of task-irrelevant perceptual sequence. A novel SRT task, the serial syllable identification task (SSI task), was used in which the participants were asked to recognize which one of two Chinese syllables was presented. The tones of the syllables were irrelevant to the task but followed an underlying structured sequence. Participants were scanned while they performed the SSI task. Results showed that, at the behavioral level, faster RTs for the sequential material indicated that task-irrelevant sequence knowledge could be learned. In the subsequent prediction test of knowledge of the tonal cues using subjective measures, we found that the knowledge was obtained unconsciously. At the neural level, the left caudate, bilateral hippocampus and bilateral superior parietal lobule were engaged during the sequence condition relative to the random condition. Further analyses revealed that greater learning-related activation (relative to random) in the right caudate nucleus, bilateral hippocampus and left superior parietal lobule were found during the second half of the training phase compared with the first half. When people reported that they were guessing, the magnitude of the right hippocampus and left superior parietal lobule activations was positively related to the accuracy of prediction test, which was significantly better than chance. Together, the present results indicated that the caudate, hippocampus and superior parietal lobule played critical roles in the implicit perceptual sequence learning even when the perceptual features were task irrelevant.