Mosquitoes are unquestionably the most medic arthropod vectors of disease. Culex pipiens, usually defined as a common house mosquito, is a well-known carrier of several virus diseases. Crude ethanol extracts of different organs of Agratum houstonianum are tested with Culex pipiens Linnaeus (Diptera: Culicidae) to determine their larvicidal, antifeedant, and repellency effects. Alongside biochemical analysis, the activity of the AChE, ATPase, CarE, and CYP-450 is detected in the total hemolymph of the C. pipiens larvae to examine the enzymatic action on the way to explain their neurotoxic effect and mode of action. Through HPLC and GC–MS analysis of the phytochemical profile of A. houstonianum aerial parts is identified. The larvicidal activity of aerial parts; flower (AF), leaf (AL), and stem (AS) of A. houstonianum extracts are evaluated against the 3rd instar larvae of C. pipiens at 24-, 48- and 72-post-treatment. A. houstonianium AF, AL, and AS extracts influenced the mortality of larvae with LC50 values 259.79, 266.85, and 306.86 ppm, respectively after 24 h of application. The potency of AF and AL extracts was 1.69- and 1.25-folds than that of AS extract, respectively. A high repellency percentage was obtained by AF extract 89.10% at a dose of 3.60 mg/cm2. A. houstonianium AF prevailed inhibition on acetylcholinesterase and decrease in carboxylesterase activity. Moreover, a significant increase in the ATPase levels and a decrease in cytochrome P-450 monooxegenase activity (− 36.60%) are detected. HPLC analysis prevailed chlorogenic and rosmarinic acid as the major phenolic acids in AL and AF, respectively. GC–MS analysis of A. houstonianum results in the identification of phytol as the major makeup. Precocene I and II were detected in AF. Linoleic, linolenic, and oleic acid were detected in comparable amounts in the studied organs. Overall, results suggest that the A. houstonianum flower extract (AF) exhibits significant repellent, antifeedant, and larvicidal activities.