Wooden structures in China’s ancient buildings hold highly historical and cultural values. There is an urgent need to repair and replace the damaged wooden structures after hundreds and thousands of years of exposure to weather. Unfortunately, to date there is still a lack of insightful understanding on how the chemical structure, composition, and micro-morphology evolve over the long-term natural aging before artificial ancient timbers can be developed. This work aims to systematically examine the outer surface, middle layer, and inner surface of the same piece of Chinese fir (Cunninghamia lanceolate) collected from an ancient Chinese building. Based on qualitative and quantitative analysis, both cellulose and hemicellulose in aged woods are found to experience significant degrees of degradation. The crystalline regions of cellulose are also determined to undergo moderate degradation as compared to the control fresh wood. In comparison, the lignin basically remains unchanged and its content in the inner layer slightly increases, as evidenced by more free phenol groups determined. Relative to the outer and inner layer, the middle layer of the ancient wood shows the lowest degree of degradation close to that of the fresh wood. This work offers guidelines for fabricating artificial ancient woods to repair the destroyed ones in China’s ancient architectures.