The Yangtze River Basin (YZRB) and Yellow River Basin (YRB) are the largest river basins in China, representing typical regions in southern and northern China. Understanding the impacts of climate and phenology on net primary productivity (NPP) is essential for regional ecological protection, management and carbon neutrality. Based on remote sensing and climate data, this study quantified the temporal trends and spatial variations in vegetation phenology and NPP. Pearson correlation and structural equation modeling were employed to examine the mechanisms through which climate and phenology influence NPP. The results reveal distinct NPP accumulation mechanisms in the YZRB and YRB. In the YZRB, the growing season significantly lengthened (0.60 days yr^-1, P < 0.05), resulting in an annual NPP increase of 3.19 gC m^-2 yr^-1, primarily driven by spring NPP (52% contribution), with direct effects of temperature (β = 0.71, P < 0.001) and radiation (β = 0.63, P < 0.001) on NPP. In contrast, the YRB exhibited balanced seasonal NPP growth (3.54 gC m^-2 yr^-1 for annual NPP), with precipitation regulating NPP through both direct and phenology-mediated indirect pathways (indirect β = 0.27, P < 0.05). These findings emphasize the complexity of the effects of climate and phenology on NPP, underscoring the necessity for region-specific management strategies to optimize productivity under climate change.