Forest ecosystem plays an important role as carbon sinks in Southwest China. Currently, remote sensing technology has been widely used to substantially model the high temporal and spatial variation in gross primary production (GPP) at a site or regional scale. However, during the growing season, the regional uncertainty of GPP in the forest ecosystem and the relative contributions of climate variations to interannual variation (IAV) of GPP are not well understood across Southwest China. Our research focuses on the joint analysis of the three-cornered hat (TCH) algorithm and uses the contribution index to analyse the model's uncertainties varying with plant functional types (PFTs), climate zones, and the contribution of climate variabilities to GPP IAV. Here, three GPP datasets are used to investigate how climate variabilities contribute to the GPP IAV during the growing season. The uncertainties in GPP vary from 829.33 g C m−2 year−1 to 2031.86 g C m−2 year−1 for different models in different climate zones and different PFTs. Additionally, the results highlight that precipitation dominates the interannual variation in GPP in forest ecosystem during the growing season in Southwest China. It makes the largest contribution (34.46%) to the IAV of GPP in the climate zone of E (cold subtropical highland area) and the largest contribution (80.83%) to PFTs of the MF (mixed forest). Our study suggests the availability and applicability of GPP products can be used to assess GPP uncertainties and analyse the contributions of climate factors to GPP IAV in forest ecosystem or other ecosystems.