We previously identified a nuclear hormone receptor gene, BmNHR96, which promotes Bombyx mori nucleopolyhedrovirus (BmNPV) entry into silkworm cells. In an attempt to create an antiviral silkworm strain for better silk production, we used RNAi to downregulate BmNHR96 in silkworm larvae. We screened the resulting BmNHR96-RNAi silkworm strain (NHR) and also explored the antiviral mechanism in vivo. We found that the survival rate of the NHR strain was higher than that of the Dazao strain, when silkworm larvae were infected with BmNPV via oral ODV infection and BV injection. More importantly, the economic characteristics (silk yield) of the transgenic line remained unchanged. These findings reveal that RNAi of BmNHR96 could be an effective way to enhance the tolerance of B. mori to BmNPV infection.