Developing an environmentally friendly and safe nanodelivery system is crucial to improve the efficacy of pesticides and minimize environmental and health risks. However, preparing a completely water-based nanopesticide without using harmful solvents is a technical challenge. In this study, a water-based nanodelivery pesticide system was constructed to improve the efficacy and safety of Emamectin Benzoate (EB). A specific surfactant, 29-(4-(5-hydroxynonan-5yl)phenoxy)-3,6,9,12,15,18,21,24,27-nonaoxanonacosan-1-ol (SurEB) was designed and synthesized to form a water-based nanodelivery system (EBWNS) with EB. Molecular dynamics simulations revealed the self-assembly and interaction forces between SurEB and EB in water, providing insights into the formation mechanism of EBWNS nanoparticles. The nanodelivery system showed the prolonged effectivity of EB with reduced degradation and demonstrated a good control efficacy for multiple target pests, such as red spider mite, beet armyworm larvae (Lepidoptera: Noctuidae), and rice stem borers (Chilo suppressalis). Toxicology tests on various objects demonstrated that the EBWNS has low toxicity for seeds, HaCaT cells, zebrafish, earthworm, and E. coli. This study provides a distinctive perspective for developing environmentally friendly nanopesticide formulations, which clarified a water-based treatment method for specific lipid-soluble pesticides. The water-based nanodelivery pesticide system has the potential to improve the efficacy and safety of pesticides in the process of field applications.