Varroa mite is one of the major adverse factors causing honey bee population decline. In this study, Varroa destructor-infested and uninfested honey bee colonies were established by selective applying miticide (Apivar® amitraz). Mite population was monitored monthly (April–October 2016), and deformed wing virus (DWV) loading was detected seasonally (April, July, and October). Four immunity- and two physiology-related gene expressions, natural mortality, and susceptibility to five insecticides were comparatively and seasonally examined in field-collected honey bee workers. Results showed that Apivar-treated bee colonies had minor or undetectable mite and DWV (using RT-qPCR) infestations in whole bee season, while untreated colonies had substantially higher mite and DWV infestations. In untreated colonies, Varroa mite population irregularly fluctuated over the bee season with higher mite counts in Jun (318 ± 89 mites dropped in 48 h) or August (302) than that (25 ± 4 or 34) in October, and mite population density was not dynamically or closely correlated with the seasonal shift of honey bee natural mortality (regression slope = −0.5212). Unlike mite, DWV titer in untreated colonies progressively increased over the bee season, and it was highly correlated (R² = 1) with the seasonal increase of honey bee natural mortality. Significantly lower gene expressions of dor, PPO, mfe, potentially PPOa and eat as well, in untreated colonies also indicated an association of increased DWV infestation with decreased physiological and immunity-related functions in late-season honey bees. Furthermore, bees with lower mite/DWV infestations exhibited generally consistently lower susceptibilities (contact and oral toxicities) to five representative insecticides than the bees without Apivar treatment. All of these data from this study consistently indicated an interaction of Varroa/viral infestations with insecticide susceptibilities in honey bees, potentially through impairing bee's physiology and immunity, emphasizing the importance of mite control in order to minimize honey bee decline.