The neural basis of learning print-to-sound mapping when Chinese is the second language is still unclear. The present study aimed to examine the neural basis of the phonological consistency effect in non-native speakers who studied Chinese as a second language (L2 learners) for at least 1 year. The fMRI results indicated that the consistency effect occurred in the left supplementary motor area and left precentral gyrus in L2 learners, but not in native Chinese speakers, suggesting that L2 learners may utilize phonological-related regions and the motor system to facilitate inconsistent character processing. These results indicated that L2 learners used assimilation for the phonological processing of Chinese characters.