Objective To investigate the effects of comprehensive intervention with peer education on acquired immunodeficiency syndrome (AIDS) prevention among female migrant workers in Shanghai. Methods Two manufactories in Pudong New Area of Shanghai similar in scale and characteristics with female migrant workers as major staff were selected, and 329 female migrant workers were enrolled by cluster random sampling method. Female migrant workers in one manufactory were served as peer education intervention group (n=211), and those in the other manufactory were served as conventional intervention group (n=118). The baseline data of two groups were obtained by questionnaire survey, and interventions were conducted respectively in both groups. Comprehensive intervention with peer education was conducted in peer education intervention group, and comprehensive intervention without peer education was carried out in conventional intervention group. Ten days after intervention, questionnaires were sent out again for evaluation of effects of intervention by scores and awareness rates of AIDS-related knowledge and analysis of influence factors by multivariate Logistic regression analysis. Results The average scores of AIDS-related knowledge in both peer education intervention group and conventional intervention group before intervention were 11, and were increased to 15 and 13, respectively after intervention. There were significant differences between scores of AIDS-related knowledge before intervention and those after intervention in both groups and between scores of two groups after intervention (P<0.05 or P<0.01). Of all the awareness rates of 17 items of AIDS-related knowledge, those of 12 and 6 items were significantly increased in peer education intervention group and conventional intervention group, respectively. Multivariate Logistic regression analysis revealed that the total score of AIDS-related knowledge after intervention was related to peer education and AIDS-related health education, and discussion on emotion and sex with workmates (P<0.05). Conclusion The effects of comprehensive peer education in AIDS prevention among female migrant workers in Shanghai are better than those of conventional intervention, and peer education is one of the independent influential factors of total score of AIDS-related knowledge after intervention.