How native and non-native languages are represented in the brain is one of the most important questions in neurolinguistics. Much research has found that the similarity in neural activity of native and non-native languages are influenced by factors such as age of acquisition, language proficiency, and language exposure in the non-native language. Nevertheless, it is still unclear how the similarity between native and non-native languages in orthographic transparency, a key factor that affects the cognitive and neural mechanisms of phonological access, modulates the cross-language similarity in neural activation and which brain regions show the modulatory effects of language distance in orthographic transparency. To address these questions, the present study used representational similarity analysis (RSA) to precisely estimate the neural pattern similarity between native language and two non-native languages in Uyghur-Chinese-English trilinguals, whose third language (i.e., English) was more similar to the native language (i.e., Uyghur) in orthography than to their second language (i.e., Chinese). Behavioral results revealed that subjects responded faster to words in the non-native language with more similar orthography to their native language in the word naming task. More importantly, RSA revealed greater neural pattern similarity between Uyghur and English than between Uyghur and Chinese in select brain areas for phonological processing, especially in the left hemisphere. Further analysis confirmed that those brain regions represented phonological information. These results provide direct neuroimaging evidence for the modulatory effect of language distance in orthographic transparency on cross-language pattern similarity between native and non-native languages during word reading.