Carbon uptake of vegetation is controlled by phenology and photosynthetic carbon uptake capacity. However, our knowledge of the seasonal responses of vegetation productivity to phenological and physiological changes in alpine ecosystems is still weak. In this study, we quantified the spatio-temporal variations of vegetation phenology and gross primary productivity (GPP) across the source region of the Yellow River (SRYR) by analyzing MODIS-derived vegetation phenology and GPP from 2001 to 2019, and explored how vegetation phenology and maximum carbon uptake capacity (GPPmax) affected seasonal GPP over the region. Our results showed that the SRYR experienced significantly advanced trends (p < 0.05) for both start (SOS) and peak (POS) of the growing season from 2001 to 2019. Spring GPP (GPPspr) had a significantly increasing trend (p < 0.01), and the earlier SOS had obvious positive effects on GPPspr. Summer GPP (GPPsum) was significantly and negatively correlated to POS (p < 0.05). In addition, GPPmax had a significant and positive correlation with GPPsum and GPPann (p < 0.01), respectively. It was found that an earlier spring-summer phenology and higher photosynthetic peak enhanced the photosynthetic efficiency of vegetation in spring and summer and altered the seasonal patterns of vegetation productivity in the SRYR under warming and wetting climates. This study indicated that not only spring and autumn phenology but also summer phenology and maximum carbon uptake capacity should be regarded as crucial indicators regulating the carbon uptake process in alpine ecosystems. This research provides important information about how changes in phenology affect vegetation productivity in alpine ecosystems under global climate warming.