Chironomid is a type of arthropod that lay eggs on objects in stagnant waters. Vertical side walls of sedimentation tanks in drink water treatment plant (DWTP) are an ideal place for it, which often leads to outbreaks of the larvae booming. Poor hygiene of drinking water and high risk of vector-borne disease are often related to maggots and adult Chironomus, which need to be effectively inhibited. Herein, a study was performed to investigate the effects of single-, dual- and triple-frequency ultrasonic radiation for the stress responses of Chironomus eggs on their viabilities, stress-related protein concentrations and antioxidative enzyme activities. Compared to the single- and dual- frequency treatments, the maximum acoustic pressure ranged from −30 pa to 12 Pa was achieved by the triple - frequency treatment. Meanwhile, the lowest integrity (25.63 %) and hatching rate (2.6 %) of Chironomus eggs were recorded after 4-min of triple-frequency treatment with 10-cm exposure distance and 450 W power. As the introduction of different frequency ultrasound, hyperoxide was generated from the effect of transient cavitation, which significant reduced activities on acetylcholinesterase (AchE), cytochrome P450, and glutathione S-transferases (GSTs) (p < 0.05), and were responsible for lysis of eggs' periplasm and shells. The work provided a commercial-scale case study to inhibit Chironomus biomass and prevent its infestation in DWTP.