Objective To investigate the prevalence of junior school students’ loneliness and the effect of family environment on it. Methods A total of 556 junior school students were investigated using Family Environment Scale (FES-CV) and Emotional-Social Loneliness Inventory (ESLI). Results In this study， 53.2% of students had emotional isolation， 39.1% had social isolation， 38.5% had emotional loneliness and 33.9% had social loneliness. Boys suffered more isolation and loneliness than girls (P ＜ 0.01). The eight grade students reported more emotional loneliness than those in seven grade (P＜ 0.05). The impact factors of emotional isolation and social isolation included cohesion， intellectual and active-recreational orientation. The impact factors of emotional loneliness and social loneliness included cohesion， conflict， active-recreational orientation and organization. Conclusions The prevalence of loneliness is common among junior school students. Family environment has important effect on adolescent loneliness.