Background The limitations associated with antipsychotics in early-onset schizophrenia patients have stimulated more interest in psychological interventions in this population. Nevertheless, the isolated psychosocial interventions are unrealistic in a treatment success covering the complex array of symptoms, and the psychosocial interventions could be an adjunct treatment to the pharmacological treatment. It is necessary to find the benefits of psychological interventions with limited and targeted use of antipsychotics. Social cognition and interaction training (SCIT) was a program for social cognitive rehabilitation in adult schizophrenia. However, it is unclear how generalizable this is to early-onset patients. Methods The current study tested this hypothesis that combined SCIT and paliperidone was superior to paliperidone alone in treating early-onset schizophrenia patients on cognitive, functional, and symptom outcomes. Two hundred eight inpatients with schizophrenia aged 13 to 17 years old participated in a 24-week work intervention program. Patients completed a battery of measures administered at a pre-SCIT intervention baseline, 4, 8, 12, and 24 weeks post-SCIT, respectively. Results SCIT had significant added benefits above paliperidone for the speed of processing, attention/vigilance, and social cognition of the Chinese version of MATRICS consensus cognitive battery (MCCB) domains (p<0.05). The following logistic regression analysis on the exploration of the influential factors also confirmed the effects of SCIT. However, combined SCIT and paliperidone intervention had a null impact on social functioning and symptomatology. Conclusions The present study provides the first evidence that combined SCIT and paliperidone intervention has the potential to improve cognitive functions for the early-onset schizophrenia patients. The findings in the current study are suggestive of the extreme importance of SCIT as an adjunctive treatment in early-onset schizophrenia patients.