Introduction: Prior research has documented the associations among phubbing, depression, and anxiety, while the cross-sectional design failed to clarify the temporal directionality of the relationships between these mental disorders and behavioral issues. To bridge this gap, the present study utilizing longitudinal data aimed to articulate the temporal relationships between these mental disorders and behavioral issues. Methods: A total of 3296 adolescents from China (54.5% girls; M[subscript age] = 15.17) participated in the study. Symptoms of phubbing, depression, and anxiety were assessed 18 months later (May 2023) after the baseline (November, 2021). The cross-sectional network and cross-lagged panel network models were conducted to explore the associations between the network structures of phubbing, depression, and anxiety. The network comparison test (NCT) was then performed to unveil whether the network structures vary based on school grade. Results: In the cross-sectional network, significant differences in the overall structures between middle and high school students were observed. For the longitudinal network, the core symptoms responsible for temporal relationships were mostly between depressive and anxiety symptoms. Phubbing-related symptoms and restlessness (anxiety symptom) were the bridge symptoms of phubbing, depression, and anxiety. Besides, the central bridges associated with phubbing-related symptoms differed significantly across different school stages. Conclusions: Successfully regulating negative emotions can play a pivotal role in tackling the root causes linked to phubbing. Apart from addressing restlessness, future interventions focusing on nomophobia and interpersonal conflict in middle school students, as well as self-isolation in high school students, contributed to mitigating phubbing, depression, and anxiety.