Effective mosquito management strategies are crucial to minimize the number of mosquito-borne diseases. Selenium nanoparticles (SeNPs) are promising in mosquito control because they are effective and eco-friendly rather than synthetic insecticides. The current study was conducted to evaluate the impact of SeNPs on the detoxification enzymes, acetylcholine esterase (AChE), glutathione S-transferase (GST), and α-carboxyl esterase (α-CarE), in larval instars of Culex pipiens complex at the LC50 concentration. In 3rd instar larvae treated with microwave-assisted selenium nanoparticles (SeNPs-MW) and gamma-assisted selenium nanoparticles (SeNPs-G), it was found that AChE activity was significantly inhibited. On the other hand, significant increases in GST and α-CarE activities were observed. Additionally, genotoxic and ultrastructure studies of midgut epithelial cells in 3rd instar larvae revealed DNA damage and cell lysis, including destruction of the cell membrane, microvilli, and nuclei. These findings suggest that SeNPs have an adverse effect on AChE gene expression, resulting in its downregulation. This downregulation can be attributed to the formation of reactive oxygen species induced by SeNPs that can modulate the host defense mechanism leading to apoptosis and subsequent larval mortality. The present study was the first to use phyto-microwave-assisted and gamma-assisted synthesis of SeNPs which provides an eco-friendly and cost-effective solution to reduce the risk of chemical insecticides. Furthermore, an integrated pest management program (IPM) using nanocides can be successfully developed for mosquito control.