The two-child policy has been implemented in China since 2016 and has attracted the attention of the world. Adolescents may face huge psychological challenges in the process of changing family structures and relationships. To date, no mental health survey of adolescents from two-child families has been conducted. We investigated the prevalence and risk factors for childhood trauma, anxiety, and depression in two-child families in a statistically representative sample of Chinese senior high school students from Shanghai. A total of 426 participants were randomly selected from 1,059 students of four senior high schools in different districts of Shanghai. The childhood trauma questionnaire-short form (CTQ-SF), self-rating anxiety scale (SAS) and self-rating depression scale (SDS) were used as the screening tools. We found that the overall prevalence of childhood trauma, anxiety, and depression among senior high school students in two-child families was 46.70% (95% CI, 39.93–53.47%), 22.17% (95% CI, 16.53–27.81%), and 35.85% (95% CI, 29.34–42.36%), respectively. The two-child families was an important factor associated childhood trauma, emotional neglect, and physical neglect (χ2 = 5.984, p = 0.014; χ2 = 4.071, p = 0.044; χ2 = 4.202, p = 0.040). Ranking in two-child families was a risk factor for childhood trauma (β = −0.135, p = 0.048). Parental preference was a significantly correlated with physical abuse, physical neglect, anxiety, and depression (β = −1.581 to 0.088, p < 0.05). Meanwhile, emotional abuse, physical abuse, emotional neglect, and physical neglect of participants in the two groups were positively correlated with anxiety and depression (r = 0.195–0.478, p < 0.05). There was a significant relationship between sexual abuse and anxiety symptoms in the one-child family group (r = 0.161, p < 0.05). The findings suggest that the overall prevalence of childhood trauma, anxiety and depression among adolescents from two-child families in China was high. The two-child families and family ranking are important factors associated childhood trauma, while parental preference is related to anxiety and depression. These results highlight an urgent need to be addressed by adolescents' mental health service providers and policy-makers.