Chitin deacetylases (CDAs) are carbohydrate esterases associated with chitin metabolism and the conversion of chitin into chitosan. Studies have demonstrated that chitin deacetylation is essential for chitin organization and compactness and therefore influences the mechanical and permeability properties of chitinous structures, such as the peritrophic membrane (PM) and cuticle. In the present study, two genes (ApCDA5a and ApCDA5b) encoding CDA protein isoforms were identified and characterized in Chinese oak silkworm (Antheraea pernyi) larvae. Although five signature motifs were identified, CDA5 proteins only have the chitin-deacetylated catalytic domain. Spatiotemporal expression pattern analyses revealed that both transcripts presented the highest abundance in the anterior region of the midgut during the feeding period after molting, suggesting their role in chitin turnover and PM assembly. The down-regulation of ApCDA5a and ApCDA5b via RNA interference (RNAi) was correlated with the breakage of chitin microfibrils in the PM, suggesting that group V CDAs were essential for the growth and assembly of the chitinous layer. Additionally, ApCDA5a and ApCDA5b may have non-overlapping functions that regulate the morphological characteristics of PM chitin construction in different ways. Larvae injected with double-stranded RNA (dsRNA) against ApCDA5a and ApCDA5b transcripts were less resistant to infection by N. pernyi than those in the control groups. These results revealed that down-regulating ApCDA5a and ApCDA5b had independent effects on the PM structure and undermined the intactness of the PM, which disrupted the function of the PM against microsporidia infection per os. Our data provide new evidence for differentiating CDA functions among group V CDAs in lepidopteran insects.