Abstract: The change of exogenous factors caused by the continuous planting broke the balance of resource allocation between the defense and growth of Cunninghamia lanceolata, which severely restricted the growth and development of Cunninghamia lanceolata and became an important constraint factor for the economic maximization of Cunninghamia lanceolata plantation in south China. The secondary metabolic regulation was an important measure for plants to respond to and resist the external stress, and was also the biochemical basis for Cunninghamia lanceolata to respond to and adapt to the continuous planting obstacles. However, the studies on the secondary metabolic basis of Cunninghamia lanceolata in response to the continuous planting obstacles were still weak, which greatly limited the understanding of the biochemical mechanisms of Cunninghamia lanceolata in response to and adaptation to the continuous planting obstacles. Through the determination of soil physical and chemical substances, seedling growth and metabolites of Cunninghamia lanceolata seedling forest in the group of continuous planting and the control group of abandoned land, the physiological basis and metabolic basis of the differential response of Cunninghamia lanceolata seedlings to the continuous planting obstacles were analyzed. The results showed that compared with the control group (abandoned land), the soil capillary porosity, total porosity, available phosphorus content, total carbon content and total nitrogen content in the group of continuous planting decreased by 23.05%, 13.22%, 73.17%, 30.23% and 24.87%, respectively. A total of 147 metabolites were detected in Cunninghamia lanceolata seedlings with each treatment. Among them, there were 87 differential metabolites, most of which belonged to the flavonoid biosynthesis pathway, and the pathway had the function of resisting the biological and abiotic stresses, indicating that the continuous planting obstacles could cause the obvious stress on the growth of Cunninghamia lanceolata seedlings, and this stress might be caused by the difference of soil capillary porosity, total porosity, available phosphorus content, total carbon content and total nitrogen content. As a result, the growth of seedling height, the growth rate of ground diameter and the growth of crown diameter decreased by 26.62%, 30.74% and 25.9%, respectively. This study explored the metabolic basis of Cunninghamia lanceolata seedlings affected by the continuous planting obstacles, which could provide theoretical basis for improving and alleviating the continuous planting obstacles of Cunninghamia lanceolata in production and for the sustainable management and scientific management of Cunninghamia lanceolata artificial forest.