The Jingtoushan Site (8300–7800 BP), located in Ningbo City, Zhejiang Province, is of great value for the in-depth understanding of China’s prehistoric coastal culture. At this site, numerous valuable wooden relics showing past human civilization have been discovered. Multiple approaches were taken, including wood anatomy and physicochemical analyses, to assess the preservation state of waterlogged archaeological woods (WAWs), while using high-throughput sequencing (HTS) to explore their microbial diversity and composition as well as that of the surrounding soil. The secondary walls of WAWs showed to be severely degraded, whereas the compound middle layer and cell corner were well preserved. Bacteria were the main microorganisms causing the biodegradation of WAWs, and 85.6% of the phyla was also found in the surrounding soil environment. Specifically, Arcobacter, Flavobacterium, Hyphomicrobium, Pseudomonas and Sphingomonas, bacteria retrieved by HTS in high abundance, were inferred to be potentially associated with the biodegradation of WAWs at the Jingtoushan Site. Meanwhile, it is hypothesized that lignin in the wooden artefacts still buried and unexcavated at the Site might be at risk of further degradation, although it may be better preserved than the cellulose and hemicellulose.