In order to assess the status of the structure of the hull of the ancient marine shipwreck, Ningbo Xiaobaijiao No.1, and to provide a scientific basis for the further protection of the shipwreck, we used optical and electron microcopy to analyze the microbial damages to the wood from the ancient marine shipwreck at the levels of microstructure and submicrostructure. We found that the microbes that had the greatest impact on the wooden relics of the shipwreck are mainly erosion bacteria (EB) and tunneling bacteria (TB), and that bacterial erosion in different wooden samples varies from slightly eroded to completely damaged. The structures of the wooden relics in different parts of the ship were evaluated by comparison with standards. The reasons for the difference in the levels of the damage of the wood artifacts were analyzed. Based on the analytical results, we have made suggestions as to how to protect the shipwrecks that have biological damage.