Social annotation has emerged as a promising approach to fostering social reading and collaborative learning. However, the implementations of social annotation vary in pedagogical depth, with some lacking structured support for deep knowledge co-construction. To address this issue, role assignment—defined as the intentional allocation of predefined roles among students—has been widely adopted to guide learner participation and foster purposeful engagement. Prior research, however, has largely relied on traditional content analysis to quantify isolated knowledge co-construction behaviors without capturing how these behaviors interrelate or unfold over time in social annotation activities. To close the gap, this study employs Epistemic Network Analysis (ENA) to reveal how three assigned roles (facilitator, synthesizer, and summarizer) contributed to students’ knowledge co-construction in social annotation activities in a university-level class. Course-wide ENA revealed that both summarizers and students without assigned roles consistently linked three core practices (Externalization, Quick Consensus Building, and Integration-Oriented Consensus Building), whereas facilitators and synthesizers consistently engaged with these three practices along with Elicitation. Building on course-wide ENA, stage-specific ENA across early, middle, and late stages further illuminated how each role’s co-construction patterns evolved over time. The results underscore the need for structured guidance and intentional instructional support to foster deeper collaborative engagement in social annotation.