Reading in a second language (L2) is a complex task that involves an interaction between L2 and the native language (LI). To investigate the fundamental mechanisms, this study used functional magnetic resonance imaging (fMRI) to visualize Japanese-Chinese bilinguals' brain activity in semantic processing of Chinese and Japanese characters, whose form are similar. We asked 13 Japanese-Chinese bilinguals to judge whether or not a presented pair of Chinese or Japanese characters had same semantics or font size. Semantic and orthographic association judgments were made to a pair of two-character words that were presented sequentially in the visual modality. In an fMRI experiment, we found Japanese-Chinese bilinguals showed activation in middle occipital gyrus in Japanese. And we also found they showed activation in left middle/inferior frontal gyrus which were known to be associated with semantic processing, left supplementary motor area which was known to solve language conflict on semantic tasks in Chinese. These findings were not consistent with previous studies that language experience tuned the cortex. But we found language conflict happened in Chinese task. This finding suggests language conflict affected Chinese task, and we think our fMRI experiment results changed from original results because of language conflict. So we think we need to remove language conflict when we conduct an fMRI experiment for bilinguals.