This study establishes a climate-sensitive transition matrix growth model and predicts forest growth under different carbon emission scenarios (representative concentration pathways RCP2.6, RCP4.5, and RCP8.5) over the next 40 years. Data from the Eighth (2013) and Ninth (2019) National Forest Resource Inventories in Chongqing and climate data from Climate AP are utilized. The model is used to predict forest growth and compare the number of trees, basal area, and stock volume under different climate scenarios. The results show that the climate-sensitive transition matrix growth model has high accuracy. The relationships between the variables and forest growth, mortality, and recruitment correspond to natural succession and growth. Although the number of trees, basal area, and stock volume do not differ significantly for different climate scenarios, the forest has sufficient seedling regeneration and large-diameter trees. The growth process aligns with succession, with pioneer species being replaced by climax species. The proposed climate-sensitive transition matrix growth model fills the gap in growth models for natural secondary forests in Chongqing and is an accurate method for predicting forest growth. The model can be used for long-term prediction of forest stands to understand future forest growth trends and provide reliable references for forest management. Forest growth can be predicted for different harvesting intensities to determine the optimal intensity to guide natural forest management in Chongqing City. The results of this study can help formulate targeted forest management policies to deal more effectively with climate change and promote sustainable forest health.