Net primary productivity (NPP) is a crucial indicator of ecosystem function and sustainability. Quantifying the response of NPP to phenological dynamics is essential for understanding the impact of climate change on ecosystem processes. In this study, vegetation phenology data for Guizhou Province were extracted from the MCD12Q2 dataset, and NPP was estimated using the Normalized Difference Vegetation Index (NDVI) combined with meteorological data. Linear regression, trend analysis, and structural equation modeling were employed to clarify the spatiotemporal patterns of NPP and phenology as a basis for exploring the role of climatic factors in the NPP’s response to phenological changes. The results indicate that 72.15% of Guizhou Province shows an increasing trend in vegetation NPP (slope = 5.0981, p = 0.002). The start of the growing season (measured as SOS) tends to advance (slope = −0.4004, p = 0.0528), while the end of the growing season (measured as EOS) tends to delay (slope = 0.2747, p = 0.1011), resulting in an overall extension of the increasing length of the season (LOS) (slope = 0.64549, p = 0.0065). The spatiotemporal patterns of SOS, EOS, LOS, and NPP varied with elevation changes. For every 500 m increase in altitude, NPP decreased by 25.3 gC/m2, SOS was delayed by 7.1 days, EOS advanced by 1.25 days, and LOS decreased by 8.36 days. These findings suggest that the response of NPP to phenological changes is primarily controlled by local climatic and topographical conditions. Additionally, the indirect effects of climate on NPP through phenological changes were more significant than the direct effects. Climatic factors play varying roles in the NPP response to phenological dynamics, highlighting the profound influence of climate in regulating the mechanisms by which NPP responds to phenological changes.