To better guide school practitioners in identifying and intervening with instances of school refusal, this study employs network analysis to investigate the core manifestations among adolescents of different genders and explores the impact of various ecological factors on these characteristics. In this study, 910 middle school students in China (Mage ± SDage = 13.55 ± 1.06, 48.13 % boys) were recruited to complete a paper-and-pencil survey on school refusal and its related factors. The least absolute shrinkage and selection operator (LASSO) method was used to examine the network characteristics of school refusal and the potential influence of ecological factors on the core characteristics of school refusal. Results revealed that: (1) the core features of Chinese students’ school refusal were “I consider studying a burden”, “I often try to find ways to avoid studying”, and “Studying often makes me feel inwardly tense and anxious”, demonstrating gender consistency; and (2) there were significant gender differences in the underlying ecological factors that influence the core characteristics of Chinese students’ school refusal. Specifically, boys’ school refusal is more related to their parental academic involvement and teacher expectations. The higher the parents’ academic involvement and teacher expectations, the lower the boys’ school refusal. Girls’ school refusal is more related to personal educational values (the value of academic success and the future utility of education). The more girls identify with the value of education, the lower their school refusal. This study utilized network analysis to reveal unique gender differences in school refusal among Chinese adolescents. It also explored the complex interrelationships between individual, familial, and school factors and school refusal, demonstrating how these factors contribute differently in boys and girls. These findings indicated potential theoretical directions for future interventions for school refusal among Chinese students of different genders.