Gross primary production (GPP) is a key indicator to evaluating ecosystem carbon sinks. Southwest China is characterised by diverse ecosystems and abundant forest resources and represents one of the most important carbon reservoirs in China. Therefore, a quantitative assessment of the uncertainty of existing GPP products and their influencing factors is important. This study investigates GPP uncertainties and its influencing factors based on the three-cornered hat (TCH) and XGBoost and SHAP methods. Thirteen products were examined, including six products from the light use efficiency (LUE) model, two products from the process-based (Process) model, three products from the machine learning (ML) model and two products from satellite-based direct proxies (Proxies). The results reveal the following: (1) All products show similar spatial patterns, with Process products fluctuating notably in 2010, 2011, and 2014, while others remain stable. (2) Relative uncertainty is lowest annually, increasing monthly and daily; ML products exhibit greater stability. Among them, CEDAR has the least uncertainty and strongest agreement with flux observations (r = 0.82), whereas EC-LUE shows the highest uncertainty. (3) Vegetation index, elevation and radiation are more influential than other factors. These findings aid GPP product selection and uncertainty assessment in complex terrains with sparse ground data.