© 2022 Elsevier B.V.Net Primary Productivity (NPP) has been widely used to estimate the productivity of the farmland ecosystem (FES) and the carbon budget of the terrestrial ecosystem. Changes in the NPP of FES have knock-on effects on food security, sustainable agricultural development, carbon sequestration, and environmental changes. Existing studies mainly focused on the impact of climate change and urbanization on the spatial-temporal pattern of NPP, largely ignoring the roles of soil condition and agricultural management practices (AMPs). At present, the joint impact of “climate-urbanization-soil-AMPs” on the NPP of FES remains unknown. To fill this knowledge gap, we use the NPP dataset retrieved by the vegetation photosynthesis model (VPM), daily meteorological records, field-collected soil data, AMPs data collected from the Government Statistical Yearbook, and land cover dataset to study the joint mechanism of “climate-urbanization-soil” that drives spatial-temporal variations of NPP. Taking the northern slope of Tianshan Mountains as the study area, our results indicate that NPP had increased by 3.86 Tg C from 2000 to 2015 (11.93 Tg C in 2000 and 15.79 Tg C in 2015). From the proposed conceptual framework, we found that climate variables (accumulated temperature, precipitation, evapotranspiration) play a major role in driving the growth of NPP (+4.01 Tg C). The AMPs (i.e., mulching filming, drip irrigation, and fertilizer application) make a positive contribution to NPP increase (+0.98 Tg C). We also found that soil salinization (-1.07 Tg C) weakens the growth of NPP more significantly than urbanization (−0.16 Tg C). This study provides new insights on the mechanism of climate change, urbanization, and soil conditions on crops, benefiting stakeholders in designing better management plans for sustainable agriculture, ecosystem cycling, and food security.