Objective: The present study explored an efficient new therapy that combined repetitive transcranial magnetic stimulation (rTMS) and family intervention in addition to risperidone to improve schizophrenia. Methods: A randomized controlled trial (January 2016���September 2017) involving 200 patients, of which 188 patients completed the 12-week study, and 50 controls were conducted in the research. The patients were randomly assigned to 12 weeks of treatment with risperidone alone (risperidone group), rTMS and risperidone (rTMS group), family intervention and risperidone (family intervention group), rTMS and risperidone plus family intervention (combined group). MATRICS Consensus Cognitive Battery (MCCB) and the Positive and Negative Symptoms Scale (PANSS) were used to evaluate treatment efficacy. Repeated measures analysis of variance (RMANOVA) were performed to evaluate different treatment efficacy between four groups after 12 weeks of treatment. Results: (1) There were no significant differences in sex, age, education, cognitive function, or PANSS scores between the four groups at baseline (p's > 0.05). (2) There was a significant decrease in the PANSS scores and an increase in the MCCB scores after 12 weeks of treatment in all groups (time effect p's < 0.001). (3) The improvements in positive symptoms and negative symptoms were more obvious in the combined group than in other groups (p's < 0.05). (4) The combined group showed the superior effect in cognition function after 12 weeks. (5) And, interestingly, a remarkable synergistic effect between rTMS and family intervention therapy was observed. Conclusion: There was a synergistic effect between rTMS and the family intervention as an effective combined therapy in improving schizophrenia. This study is registered with Chictr.org, number ChiCTR1900024422 (http://www.chictr.org.cn/edit.aspx?pid=34285&htm=4).