As a key biotic factor, phenology exerts fundamental influences on ecosystem carbon sequestration. However, whether spring phenology affects the subsequent seasonal ecosystem productivity and the underlying resource limitation mechanism remains unclear for the alpine grasslands of the Tibetan Plateau (TP). In this study, we investigated the direct and lagged seasonal responses of net primary productivity (NPP) to the beginning of growing season (BGS) along a precipitation gradient by integrating field observations, remote sensing monitoring and ecosystem model simulations. The results revealed distinct response patterns of seasonal NPP to BGS. Specifically, the BGS showed a significant and negative correlation with spring NPP (R = −0.73, p < 0.01), as evidenced by the direct boosting effects of earlier BGS on spring NPP. Moreover, spring NPP was more responsive to BGS in areas with more annual precipitation. The boosting effects of earlier BGS on NPP tended to weaken in summer compared with that in spring. Sequentially, BGS exhibited stronger positive correlation with autumn NPP in areas with less annual precipitation, which suggested the enhanced lagged suppressing effects of earlier spring phenology on ecosystem carbon assimilation during the later growing season under aggravated water stress. Overall, the strengthened NPP in spring was offset by its decrement in autumn, resulting in no obvious relationship between BGS and annual NPP (R = −0.34, p > 0.05) for the entire grasslands on the TP. The findings of this study imply that the lagged effects of phenology on the ecosystem productivity during the subsequent seasons should not be neglected in the future studies.