To investigate the molecular mechanisms of cytoplasmic incompatibility (CI) induced by Wolbachia bacteria in Drosophila melanogaster, we applied an isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomic assay to identify differentially expressed proteins extracted from spermathecae and seminal receptacles (SSR) of uninfected females mated with either 1-day-old Wolbachia-uninfected (1T) or infected males (1W) or 5-day-old infected males (5W). In total, 1317 proteins were quantified; 83 proteins were identified as having at least a 1.5-fold change in expression when 1W was compared with 1T. Differentially expressed proteins were related to metabolism, immunity, and reproduction. Wolbachia changed the expression of seminal fluid proteins (Sfps). Wolbachia may disrupt the abundance of proteins in SSR by affecting ubiquitin–proteasome-mediated proteolysis. Knocking down two Sfp genes (CG9334 and CG2668) in Wolbachia-free males resulted in significantly lower embryonic hatch rates with a phenotype of chromatin bridges. Wolbachia-infected females may rescue the hatch rates. This suggests that the changed expression of some Sfps may be one of the mechanisms of CI induced by Wolbachia. This study provides a panel of candidate proteins that may be involved in the interaction between Wolbachia and their insect hosts and, through future functional studies, may help to elucidate the underlying mechanisms of Wolbachia-induced CI.