Summary Ginkgo biloba L., a long-lived relict species, has high ecological, cultural and economic value. Studying the quantitative wood anatomy of G. biloba is important to understand the relationships between their tree-growth and climate change, which could help in the protection of old G. biloba trees. Preparing high-quality wood thin sections is the premise of quantitative wood anatomy analysis. In addition, manual correction of image analysis is a time-consuming process. We therefore present a protocol on how to make G. biloba high-quality xylem thin sections, from sample preparation, sample embedding, blade selection to thickness selection. We also present a method to determine the necessary sample width and number of cores to establish reliable wood anatomical time series that both can capture climate signals and reduce the time used for image analysis. For microsection preparation, it is optimal to cut 20–30-μm-thick sections using Leica DB80 blades after applying the cornstarch solution on top of the sample surface. For image analysis, the reliable wood anatomical time series can be established when measuring six cores (trees) or above, and the environmental signals are captured when analyzing a 1.2-mm-wide radial strip along the increment core (deviation <2%) for the parameters cell density, mean lumen area, potential hydraulic conductivity and percentage of the conductive area. This paper provides practical guidance to successfully use quantitative wood anatomy methods on G. biloba. We hope our study will be helpful for future research on the quantitative wood anatomy of G. biloba and similar tree species.