Background: While there is research on protective factors against smartphone addiction (SA) and phubbing, which impact adolescents’ physical, psychological, interpersonal, and academic well-being, focused studies on these issues among Thai Muslim students in Southern Thailand remain scarce. Objectives: To bridge this gap, this research aimed to explore the influence of five family functioning factors—discipline, communication and problem-solving (CPS), relationship, emotional status, and family support—guided by family systems theory and the McMaster Model, on SA and phubbing. Methods: Data from 825 Thai Muslim adolescent secondary school students (Female N = 459 (55.7%), Mage = 15.11 ± 1.78) across three southern Thai provinces were analyzed utilizing structural equation modeling (SEM). Results: Significant connections were identified between family functioning factors, particularly emotional status and discipline, and SA, and their impact on phubbing behavior. SA was found to mediate the relationship between these two family factors and phubbing. Interestingly, a higher quality of family relationships was found to be associated with an increased risk of SA, while the other two family functions—CPS and family support—demonstrated no significant association with these digital behaviors. Conclusions: Despite its limitations, including a cross-sectional design and reliance on self-reports, the study underscores the importance of specific family functions in preventing and addressing adolescent SA and phubbing.