“Nanhai No.1” is a wooden merchant ship from the Southern Song Dynasty of China. It sank about 20 nautical miles south of Dongping Port in Yangjiang City, Guangdong Province. It was discovered in 1987. After several underwater archaeological investigations, it was strictly followed in 2007. Under the archaeological regulations, it was successfully salvaged out of the water. So far, the oldest, largest and most intact ancient sunken ship has been discovered in China. During longtime in seabed and damaged by seawater, the waterlogged archaeological wood have undergone serious physical, chemical and biodegradation effect by salt in the seawater and various microorganisms. It is give rise to wood components are degraded and eroded, and the supporting force between wood fibers is reduced, resulting in reduced strength and decayed structure. The accumulation of sulfur and iron considered to be associated with bacterial degradation of the wood. Iron sulfides can be oxidized to form sulfuric acid, which damages the wood cellulose and results in the degradation of organic materials. Thus, the content, distribution, and occurrence of iron and sulfur elements have important academic value for the research and protection of organic materials under sea. Due to sample preparation and method limitations, traditional methods make it difficult to perform in-situ and non-destructive analysis of iron/sulfur in waterlogged wood. Also, analysis speed and cost are also hard to overcome. μ-X-ray fluorescence, especially micro-focusing technology based on commercial X-ray tubes, provides a more convenient, fast, reliable, non-destructive and low-cost solution to this problem. Based on the opinion, selected the samples of the “Nanhai No.1” shipwreck hull, applied the latest multi-capillary μ-X-ray fluorescence spectroscopy technology, combined with Raman spectroscopy analysis, and conducted a surface scan analysis of the iron and sulfur content and distribution in the waterlogged archaeological wood. The results indicate that the distribution of iron and sulfur elements in the sample is heterogeneous, and there are multiple occurrence forms. The characteristics and rules of element distribution provide clues to reveal the sources, enrichment and coupling relationships of sulfur and iron in waterlogged wood. Studies have shown that μ-XRF technology can effectively analyze the iron and sulfur abundance in different parts of irregular and uneven waterlogged wood and reveal the distribution of elements and their correlation on a two-dimensional scale.