The synergistic use of chemical pesticides and biological agents poses the fundamental challenge of balancing control efficacy with ecological safety. In recent years, nanotechnology has emerged as a promising strategy for improving pesticide performance while reducing pesticide residues and alleviating environmental contamination. Herein, we developed an efficient nano-pesticide based on star polycation (SPc) loaded with clothianidin, which was co-applied with a widely used parasitic wasp (Aphidius colemani) to achieve synergistic pest management. SPc at the working concentration displayed no significant impact on the eclosion or survival of parasitic wasps, whereas the oral feeding of SPc at an extremely high concentration significantly up-regulated several genes related to ribosomal protein and energy metabolism, leading to metabolic imbalance and subsequent mortality of the parasitic wasps. The SPc could load clothianidin via hydrogen bonding and Van der Waals forces, and this spontaneous complexation achieved a reduction in particle size from 6,554.87 to 467.84 nm. Importantly, the clothianidin/SPc complex exhibited a 16–28% increase in insecticidal activity against green peach aphids (Myzus persicae), while showing minimal adverse impacts on the eclosion and parasitism of parasitic wasps. Finally, co-application of the clothianidin/SPc complex with parasitic wasps achieved up to 80% mortality in green peach aphids, with the promising advantages of rapid pest suppression and sustainable control. This study proposes a synergetic pest management strategy based on nano-pesticides and natural enemies, which is beneficial for maintaining long-term agricultural ecological balance.