Impregnation with biocides is an efficient approach to prolong the service life of wood materials, but most biocides pose a toxic threat to human health and the environment. This study presents a novel and green system for protecting Masson pine and pond cypress against the brown-rot fungus Gloeophyllum trabeum through a combination of 4,5-dichloro-2-n-octyl-3-isothiazolinone (DCOI) and chelators with high iron affinity. As results, both diethyltriaminepentaacetic acid (DTPA) and tetrasodium iminodisuccinate (IDS) reduced the mass losses of Masson pine and pond cypress, but neither chelator inhibited the growth of G. trabeum at a low concentration. The compound system was more efficient in reducing the mass loss of Masson pine compared to DCOI alone. Moreover, the DCOI degradation rate decreased significantly by IDS, suggesting that chelators with high iron affinity can protect organic biocides from degradation. All data supported that the chelators were able to enhance the organic biocide in improving wood decay resistance, and the involved mechanism was mainly due to the restriction on iron-based Fenton chemistry deployed by brown-rot fungi. This study provides valuable insight into the development of environmentally benign techniques to preserve wood.