Tree stems may be a significant source of atmospheric methane (CH4), and the heartwood CH4 concentration determines the magnitude of CH4 emissions from tree stems. However, our understanding of heartwood CH4 concentrations and bacterial community composition remains limited. In this study, we investigated the heartwood CH4 concentration characteristics at four sites (upland, peatland, swamp, and riparian zone) in the permafrost zone of the Great Hing’an Mountains and compared the differences between the two by distinguishing between broadleaf and coniferous trees. Relevant datasets (N = 355) of global heartwood CH4 concentrations were collected through literature search and screening to test our results. In addition, the bacterial community composition in bark and cores was determined by high-throughput sequencing. The results showed that heartwood CH4 concentrations were consistently higher in broadleaf trees than in conifers, both in the present study and based on literature statistics. The heartwood CH4 concentrations were lower in this study, ranging from (1.54 ± 0.15) to (2.17 ± 0.22) μL/L. Identical and respective endemic genera were found in the heartwood and bark bacterial communities, with common genera belonging to the order Chloroplast, family Mitochodria、Pectobacteriaceae and three genera that have not yet been identified. In particular, we found the endemic genus methane oxidising bacteria (Methylocella) in the bark. These plant endophytes not only promoted plant nutrient uptake and maintain the plant health dynamic, but may also had a potential impact on tree stems CH4 balance, and future studies need to carry out further field observations to explore the characteristics of tree stems CH4 flux changes in this region. This study clarified the heartwood CH4 concentration characteristics changes and bacterial communities of the heartwood and bark in the permafrost zone of the Great Hing’an Mountains, which not only provided a scientific basis and data support for in-depth knowledge of the dynamics of tree stems CH4 in this region, but also provided a reference basis for the prevention and control of tree diseases.