Synaptic hypothesis of schizophrenia suggests that alterations of synaptic transmission and neuronal connectivity might be core feature of schizophrenia. STON2 participates in synaptic vesicle protein recognition and neural endocytosis. To explore the association of STON2 with schizophrenia, 11 single nucleotide polymorphisms (SNPs) were examined in 768 Chinese Han schizophrenia cases and 1347 Chinese Han controls. The results showed that three SNPs had strong association with schizophrenia, two exonic SNPs (rs2241621: allelic P=0.0005; rs3813535: allelic P=0.0078) and one intronic SNP (rs9323698: allelic P=0.0019). When haplotype analysis performed, two linkage disequilibrium blocks showed significant differences in frequency between cases and controls. Notably, our data displays an over-transmitted functional haplotype C-C (Pro307-Ala851) in schizophrenia cases. Our results suggest STON2 may be a susceptibility gene for schizophrenia.