Background: Executive function (EF) plays a crucial role in children's reading. However, previous studies were based on offline products of reading comprehension. Online research is needed to reveal the core mechanisms underlying children's reading processing. By measuring children's working memory (WM) and cognitive flexibility (CF), we investigated whether individual differences in EF could modulate sentence processing and, if so, how they exert their roles. Methods: The present study manipulated semantic congruency and the association between crucial words in a sentence. We recruited 89 Chinese children aged 9-12 years and monitored their eye movement. Results: The study revealed distinct associations between reader- and text-related characteristics, as evidenced by eye-movement patterns during reading. A significant incongruency effect was observed in reading, underscoring the children's capacity to discern incongruent information. Children's WM and CF were found to modulate this process. Specifically, high-WM children showed more effective integration of incongruent information when the textual context was closely related during the later-stage processing. In contrast, low-WM children faced more challenges with incongruent words. Additionally, CF was influential during the early processing period. High-CF children exhibited longer early-stage reading times for incongruent words in associated contexts. Conclusions: Individual differences in EF can modulate children's online sentence processing. However, different EF components may play different roles.