The microsporidium Nosema bombycis is an obligate intracellular parasite of Bombyx mori and causes serious losses in the sericulture industry. The isobaric tags for relative and absolute quantitation (iTRAQ) methods have been used to study numerous pathogen-host interactions. Here, using iTRAQ technology, we explored the quantitative proteomics by gene ontology and KEGG. The proteins in the ovaries of B. mori infected with N. bombycis were identified and compared to those in uninfected ovaries by iTRAQ. A total of 5401 proteins were identified, and 70 of them were differentially expressed. The differentially quantified proteins were involved in a variety of important processes and pathways, such as host development, host metabolism or host defense system. Most proteins involved in basic metabolism were up-regulated following infection, and the expression levels of some proteins related to the host immunity, such as the lipid droplet protein prilipin, 30 K proteins, HDD13, and beta-1,3-glucan recognition protein, were altered after infection with N. bombycis. Juvenile hormone acid methyltransferase, which regulates insect development, and ATG8, which is a key factor in autophagy, were also induced by N. bombycis infection. Our comparative and quantitative proteomic data will provide new insights into the interaction between N. bombycis and B. mori, especially in the host ovary.