In the present study Syzygium aromaticum essential oil (EO) was extracted using water as a solvent and encapsulated within chitosan nanoparticles, which are characterized by Ultraviolet-Visible (UV-VIS) spectra, Infra-Red (IR), Transmission Electron Microscopy (TEM), and X-ray diffraction (XRD). The insecticidal activity for both Syzygium aromaticum bulkEO and encapsulated EO within chitosan nanoparticles was determined. Both of the two oil forms were assessed as a larvicide against third instar larvae of Culex pipiens by measuring LC values. Encapsulated nano-formulation EO showed higher toxicity (LC₅₀ =20 ppm) than the bulk EO (LC₅₀ =39 ppm). The biochemical changes were measured after treatment with both forms of EO.  There is an increase in the activity of three enzymes (acid phosphatase, alkaline phosphatase, and glutathione-S-transferase), while the activity of acetylcholinesterase was decreased. The obtained results revealed that water extract of Syzygium aromaticum EO and nano-encapsulated EO may be promising alternative larvicide for controlling Culex pipiens larvae in integrated pest management.