Emotion perception is essential to affective and cognitive development which involves distributed brain circuits. Emotion identification skills emerge in infancy and continue to develop throughout childhood and adolescence. Understanding the development of the brain’s emotion circuitry may help us explain the emotional changes during adolescence. In this work, we aim to deepen our understanding of emotion-related functional connectivity (FC) from association to causation. We proposed a Bayesian incorporated linear non-Gaussian acyclic model (BiLiNGAM), which incorporated association model into the estimation pipeline. Simulation results indicated stable and accurate performance over various settings, especially when the sample size was small. We used fMRI data from the Philadelphia Neurodevelopmental Cohort (PNC) to validate the approach. It included 855 individuals aged 8–22 years who were divided into five different adolescent stages. Our network analysis revealed the development of emotion-related intra- and intermodular connectivity and pinpointed several emotion-related hubs. We further categorized the hubs into two types: in-hubs and out-hubs, as the center of receiving and distributing information, respectively. In addition, several unique developmental hub structures and group-specific patterns were discovered. Our findings help provide a directed FC template of brain network organization underlying emotion processing during adolescence. Author Summary Our study introduces a novel method for analyzing directed graphs across multiple groups and demonstrates its effectiveness through a series of simulation studies. This method is applied to investigate the development of directed functional connectivity for emotion processing across diverse adolescent periods. Our findings unveil a notable increase in interfunctional connectivity with age, specifically involved with the executive control and memory retrieval, indicating the maturation of emotion processing function. Additionally, significant development of intraconnectivity in the subcortical areas emerges in early adolescence, whereas development of cerebellum emerges in the very end of adolescence. These insights offer valuable contributions to our understanding of the dynamic neural processes underlying emotion regulation during adolescence.