Shipwreck wood often contains soluble salts and iron sulfides, which pose a threat to its stability. Therefore, desalination treatment must be carried out during protection. In this study, deionized water and ethylene diamine tetraacetic acid disodium salt (EDTA-2Na) solution were used to extract soluble salts and iron sulfides from the 511 wood components of the “Huaguangjiao I” shipwreck. The extraction lasted for 1120 days, during which extraction progress was monitored by measuring the electrical conductivity and iron content of the soaking solution. The results indicated that the extraction experiment reached its endpoint when the conductivity of the soaking solution was maintained at 80~100 μs/cm and the iron content was maintained at 8~15 mg/L. More than 143.35 kg of iron were extracted from the wood of the “Huaguangjiao I” shipwreck. After extraction, the content of soluble salt ions in the wood were less than 5 μg/g, with an iron content below 5%. The wood has returned to its original color and with a certain degree of degradation. “Huaguangjiao I” was the first large-scale marine shipwreck to complete the desalination treatment of all wooden components. This study provides guidance for the desalination treatment of large-scale wooden shipwrecks.