Objective Social structure and social capital are important variables for public health strategies seeking to prevent smoking among adolescents. The purpose of this study was to examine the relationships between social structure, social capital and changes in smoking status from the 8th to 9th grade in Taiwan. Methods Data were obtained from the Child and Adolescent Behaviors in Long-term Evolution (CABLE) project. The study analyzed a final sample of 1937 students (50.7% female). Results Each layer of social structure was associated with a particular form of social capital. Students whose parents were married and living together had higher family social capital. After controlling for background variables, the social structure variable of friends who smoke was significantly associated with changes in smoking status. Students reporting more school attachment were less likely to start smoking. Students with higher parental supervision was associated with less chance of being a consistent smoker, whereas participation of social organization outside of school was associated with continued smoking. Attending school club was associated with higher probability of smoking cessation. Conclusion Smoking prevention and intervention strategies aimed at junior high school students should be tailored to the particular form of social capital important for each type of smoking status.