An ancient Banjing-river ship was excavated in an offshore river channel in Taicang. Desalination treatments are usually required before conservation and restoration work is carried out. In order to fully understand the salt content of the ship’s wood, the types and amounts of salts in samples from different parts and of different tree species were tested and analyzed. The results show that the insoluble salts contained in ship wood were represented by sulfur and iron compounds, with some containing FeS₂ (pyrite). The darkening of the ship wood is related to the iron ions in ship materials. The iron ions mainly come from iron nails on the ship and metal chelators are used to chelate and remove them. Through a comparative study of the effects of EDTAHO (EDTA-2Na and H₂O₂ compound reagent), EDTA-2Na and NaH₂PO₄·2H₂O soaking methods, the comprehensive effect of desalination using a 1 000 mL 0.4% neutral EDTA-2Na solution was the best. The iron ion concentration could be controlled within 1 mg/L after desalination twice in 44 days. Calculation of color difference (ΔE) using the L, a and b values of the samples obtained by a portable colorimeter after desalination showed the proximity to that of healthy material. The damage caused to synthetic cellulose and lignin was the least. In the end, EDTA-2Na was selected as the insoluble salt removal reagent for the ancient ship. The results of this study could provide favorable conditions for subsequent preservation work.