Social and emotional skills play a crucial role in students’ human capital development. Based on field survey data from 13 counties in three prefectures of a province in Northwestern China, this study investigates the status and determinants of primary school students’ social and emotional skills in disadvantaged areas. The results show that, first, female students, left-behind children, non-boarding students, and those from non-single-parent families, as well as students with higher parental education levels and better family economic conditions, exhibit higher social and emotional skill scores. Second, family assets, supportive parenting, parent-child communication, playing with friends, and reading extracurricular books positively influence social and emotional skills, while punitive parenting and activities such as internet use and mobile phone gaming are negatively associated with students’ social and emotional skills. Third, social and emotional skills are significantly correlated with math performance, sense of school belonging, teacher-student relationships, school bullying, and mental health. Fourth, international comparisons reveal that students from Suzhou outperform most of their international peers in social and emotional skills, while students in rural Northwestern China demonstrate average levels of agreeableness but lag behind in other dimensions. Furthermore, on a global scale, female students, high-achieving students, and those from wealthier families generally outperform their counterparts. This highlights the need to prioritize the development of social and emotional skills among rural students with limited educational resources, emphasizing the importance of collaboration between schools and families to foster holistic development.