With the development of information and communication technology, project-based learning (PBL) has become an important pedagogical approach. Group leaders are critical in PBL, and prestige influences learner leadership. Regulation affects learners' prestige, but research on their relationship is lacking. Through content analysis and epistemic network analysis, we examine the regulatory patterns of 21 learners engaged in multi-layered online PBL through online collaborative learning activities over 14 weeks. The analysis results show that: (1) High-prestige learners engaged significantly in "socially shared regulation (U = 24.0, Z = -2.183, p = 0.029)", "monitoring (U = 26.5, Z = -2.008, P = 0.043)", "task understanding (U = 15.0, Z = -2.829, p = 0.004)", and "organizing O (U = 20.5, Z = 0.015, p = 0.013)". (2) The regulatory patterns during PBL stages show that high-prestige learners focus on task dimensions in intra-group discussions. (3) High-prestige learners display positive emotions in inter-group assessments and intra-group refinements. In contrast, low-prestige learners exhibit higher negative emotional engagement. (4) There is a strong correlation between socially shared regulation (GRG = 0.780), content monitoring (GRG = 0.728), and learners' prestige. Socially shared regulation (p = 0.001), self-regulation (p = 0.001), monitoring (p = 0.006), evaluation (p = 0.019), content monitoring (p = 0.000), and process monitoring (p = 0.018) all significantly positively impact learners' prestige. The findings suggest that providing self-regulation and socially shared regulation scaffolding for PBL and utilizing various other methods to enhance learner regulation of learning are likely to increase learners' prestige and PBL effectiveness.