Family structure is of special interest in understanding adolescent health. However, while the family structure is becoming more diverse in China, much of the research has overlooked more complex types of family structure and the indirect association between family structure and adolescent health. The purpose of the present study was to examine the association between family structure and adolescent health and to identify the indirect roles of family income and parent–child communication in this association. Data were obtained from the 2014 to 2015 China Education Panel Survey (CEPS). The analytic sample included 9091 adolescents. The results showed that relative to two-parent families, the self-reported health of adolescents in non-two-parent families was poorer. Family income and parent–child communication played indirect roles in the relationship between family structure and adolescents’ self-reported health. Several gender differences were also found. Single-mother families and reconstituted families were negatively associated with sons’ self-reported health, while daughters showed worse health status in all types of non-two-parent families. Switching from a two-parent family to a non-two-parent family was correlated with a decline in adolescent girls’ self-reported health.