In arid and semi-arid climate zones, understanding the spatial patterns and biogeographical mechanisms of net primary production (NPP) and precipitation use efficiency (PUE) is crucial for assessing the function and stability of ecosystem services, as well as directing ecological restoration. Although the vegetation coverage has changed dramatically after the construction of several ecological restoration projects, due to limited observation data, fewer studies have provided a thorough understanding of NPP and PUE’s recent spatial patterns and the controlling factors of different vegetation types in the Yellow River Basin (YRB). To narrow this gap, we integrated remote-sensing land-cover maps with long-term MODIS NPP and meteorological datasets to comprehend NPP and PUE spatial patterns in YRB. Furthermore, we applied structural equation models (SEM) to estimate the effect intensity of NPP and PUE controlling factors. The results showed that along geographical coordinates NPP and PUE decreased from southeast to northwest and trends were roughly consistent along latitude, longitude, and elevation gradients with segmented patterns of increasing and decreasing trends. As for climate gradients, NPP showed significant linear positive and negative trends across the mean annual precipitation (MAP) and the arid index (AI), while segmented changes for PUE. However, the mean annual average temperature (MAT) showed a positive slope for below zero temperature and no change above zero temperature for both NPP and PUE. SEM results suggested that AI determined the spatial pattern of NPP, whereas PUE was controlled by MAP and NPP. As the AI becomes higher in the further, vegetation tends to have decreased NPP with higher sensitivity to water availability. While artificial vegetation had a substantially lower NPP than original vegetation but increased water competition between the ecosystem and human society. Hence further optimization of artificial vegetation is needed to satisfy both ecological and economic needs. This study advanced our understanding of spatial patterns and biogeographic mechanisms of NPP and PUE at YRB, therefore giving theoretical guidance for ecological restoration and ecosystem function evaluation in the face of further climate change.