Net Ecosystem Productivity (NEP) is an important measure to assess the carbon balance and dynamics of ecosystems, providing a direct measure of carbon source–sink dynamics in terrestrial ecosystems and finding widespread applications in carbon cycle research. However, the nonlinear characteristics of NEP in Xinjiang’s terrestrial ecosystems remain unclear. Additionally, the influence of land use patterns, temperature, and precipitation variations on carbon sink capacity remains unclear. Ensemble Empirical Mode Decomposition (EEMD) is used to investigate the nonlinear variation of NEP in Xinjiang. Landscape pattern analysis of Xinjiang’s land use patterns from 1981 to 2019 is conducted using a 30 km moving window, and the interannual relationships between NEP, land use patterns, and meteorological factors are investigated through EEMD detrending analysis and Pearson correlation. The findings indicate that: (1) NEP exhibits interannual variations, primarily concentrated in the foothills of the Tianshan Mountains, with a three-year cycle. (2) Although NEP changes in most regions are not significant, urban clusters on the northern slopes of the Tianshan Mountains show noteworthy trends, with initial decrease followed by an increase, covering around 34.87% of the total area. Areas at risk of NEP decline constitute approximately 7.32% of the total area. (3) Across Xinjiang, we observe a widespread rise in patch fragmentation and complexity, coupled with a decline in patch connectivity and the size of the dominant patch. Additionally, there is a notable increase in both the diversity and evenness of land use types. However, the correlation between land use patterns and NEP is generally found to be insignificant in the majority of areas, with a percentage exceeding 85%. (4) Approximately 62% of regions in Xinjiang have NEP that is positively correlated with temperature, with significance observed in 33% of these areas. Furthermore, almost 95% of regions demonstrate that NEP is positively correlated with precipitation, with significance noted in 83% of these regions. It appears that precipitation exerts a more pronounced influence on NEP fluctuations in Xinjiang when compared to temperature.