The development of interactive e-modules as digital learning materials has transformed how university students read and comprehend academic information, yet their ability to navigate non-linear digital texts containing hyperlinks and multimodal elements remains a significant challenge. This study aimed to analyze students' reading strategies in navigating non-linear digital texts within interactive e-modules, identify the challenges encountered, and examine the relationship between reading strategies and reading comprehension. The study employed a mixed-methods approach with an evaluative-participatory design involving 60 undergraduate students in an Indonesian Language and Literature Education program. Data were collected through digital navigation logs, think-aloud protocols, metacognitive reflections, and digital reading comprehension tests. Findings revealed that selective hyperlink navigation was the most frequently used strategy and produced the highest comprehension scores. Students employing directed-branching navigation patterns demonstrated better comprehension than those using linear or random navigation. The main challenges included excessive hyperlinks, difficulty identifying relevant information, and increased cognitive load during reading. Effective digital reading was influenced by the interaction among metacognitive strategies, navigation quality, and non-linear text structure. The novelty of this study lies in integrating reading strategy analysis, digital navigation patterns, and comprehension levels within the context of interactive e-modules, offering implications for developing digital learning materials that are more adaptive to digital readers' characteristics.