The northern slope of the Tianshan Mountains in Xinjiang was an important agricultural production base in China's northwestern arid region, and in recent years it had been strongly affected by climate change and water-fertilizer management measures. The region exhibits a distinct warming and wetting trend, coupled with continuous optimization of water and fertilizer management measures, which have collectively led to significant changes in farmland ecosystem productivity. Against this backdrop, it is of great significance to elucidate the coupling mechanisms between climate change and water-fertilizer management measures in agricultural ecosystems, and to formulate science-based management strategies that mitigate the impacts of climate change on arid farmlands, thereby safeguarding regional food security and leveraging the strengths of the nation as a major agricultural player. This study localized the physiological and ecological parameters of major crops and management module parameters in the Tianshan North Slope using the Biome-BGC MuSo model. It revealed the spatiotemporal distribution characteristics of net primary production (NPP) in the Tianshan North Slope farmland ecosystem from 1979 to 2018, quantified the relative contributions of climate change and water-fertilizer management measures to NPP, and investigated the response of NPP to different irrigation and fertilization measures. The results indicated that: (1) From 1979 to 2018, NPP in the agricultural ecosystems of the northern slope of the Tianshan Mountains increased before decreasing, with 2011 as the dividing point, and the multi-year average value was 0.409 kg C m^-2 a^-1. High NPP values were primarily concentrated in the southern part of Qitai County and Wenquan County, where corn and wheat were the main crops; low-value areas were more dispersed, found in the northern part of Wusu City, Shaowan County, and Manas County, where cotton was the primary crop. (2) Climate change and management measures contributed 38.75% and 61.25%, respectively, to the NPP of the farmland ecosystem on the northern slope of the Tianshan Mountains., and scientifically sound management measures could effectively amplify the positive effects of climate change on NPP and mitigate its negative impacts. (3) The NPP of corn, wheat, and cotton increased initially and then plateaued with increasing irrigation and fertilizer application. An irrigation volume of 475 mm and a fertilizer application rate of 236 kg/hm² (1.3 times the baseline rate) constituted the optimal water-fertilizer management combination. Beyond this threshold, the increase in crop NPP weakened significantly. The study results provided theoretical references for arid region farmland ecosystems to adapt to climate change and maintain regional sustainable development.