Residues of iprodione, used for the control of fungal diseases in crops, endanger both human health and ecosystem functioning. In this study, we isolated an iprodione-degrading bacteria, Pseudarthrobacter sp. Y-5, able to grow on iprodione as the sole carbon source. To achieve the high-level stable synthesis of iprodione hydrolase (IpaH), an unmarked genetic engineering approach was used to construct Bacillus subtilis WB800-ipaH, which showed the extracellular secretion and expression of the ipaH gene. Strain WB800-ipaH had superior degradability and showed cost-effectiveness potential for the bioremediation of iprodione-polluted environments than those of strain Y-5. Furthermore, iprodione suppressed Chlorella ellipsoidea growth and was toxic to Daphnia magna, while strains Y-5 and WB800-ipaH were both capable of degrading iprodione to relieve its toxicity. Both Y-5 (107 CFU g−1 soil) and WB800-ipaH (105 CFU g−1 soil) could eliminate >90% of 5 and 20 mg kg−1 iprodione in field soil within 9 d and 15 d, respectively. This work provides strain resources for eliminating the residue of iprodione in the environment.