With the advent of sequencing technology, characterization of schizophrenia with underlying probing of gut microbiome can provide abundant clues for diagnosis and prognosis of schizophrenia. In this study, we first compared the difference of gut microbiota between schizophrenia patients and healthy controls by 16S rRNA sequencing. We further explored whether gut microbiota can be used as a biomarker to assist in the diagnosis of schizophrenia. We restricted inclusion criteria strictly to control confounding bias. Finally, we investigated differences in fecal microbiota between 64 schizophrenia patients and 53 healthy controls. At the phylum level, we found that the abundance of Proteobacteria in the schizophrenia patients was significantly increased. At the genus level, the relative abundance of Succinivibrio, Megasphaera, Collinsella, Clostridium, Klebsiella and Methanobrevibacter was significantly higher whereas the abundance of Blautia, Coprococcus, Roseburia was decreased compared to health controls. The receiver operating characteristic curve analysis demonstrated that 12 significant microbiota biomarkers were capable of being used as diagnostic factors for distinguishing the schizophrenia cohort from those in the control cohort (AUC = 0.837). We performed PICRUSt analysis and found that several metabolic pathways differed significantly between healthy controls and schizophrenia patients, including vitamin B6 and fatty acid. In conclusion, there are some difference of gut microbiota between schizophrenia patients and healthy controls and the insights from this study could be used to develop microbiota-based diagnosis for schizophrenia.