In this study, 166 Xinjiang Uygur bilingual children in grades 3 to 5 were selected for testing. SPSS stepwise regression analysis was used to explore the effects of phonological awareness and working memory on reading fluency after controlling for the autoregressive effects of general cognitive ability and morpheme awareness. The results showed that: (1) Phonological awareness and working memory were significantly positively correlated with reading fluency. (2) Phonological awareness and working memory had the ability to predict the reading fluency of Uygur children, and phonological awareness had the best predictive ability (47.8%). This finding suggests that phonological awareness and working memory are two important factors in reading fluency. What’s more, cognitive skills have different effects on different reading situations. (3) Finally, this study also demonstrates a third research question, i.e., the correlation between phonological awareness, working memory, and reading fluency, as well as grade differences. The results show that the phonological awareness and working memory of Uygur bilingual children play an important role in reading fluency, and they change with age.