The present study aims to examine the contribution of cognitive flexibility to metalinguistic skills and reading comprehension during primary school years. Forty-nine third-grade primary school children completed the measures of cognitive flexibility, metalinguistic skills including syntactic awareness (word order knowledge), morphosyntactic skill and discourse awareness (sentence order knowledge), and reading comprehension. Hierarchical regression analysis results showed that syntactic awareness, morphosyntactic skill, discourse awareness and cognitive flexibility are significantly predictive of reading comprehension. However, cognitive flexibility is a unique predictor of reading comprehension over and above age and all other metalinguistic measures. Cognitive flexibility is insignificantly associated with syntactic awareness, morphosyntactic skill, and discourse awareness. The results extended the understanding of the role of cognitive flexibility in the reading comprehension process.