Vulnerable ecological regions in China represent vast territories with significant potential for augmenting carbon sinks. The widespread recognition of net primary productivity (NPP) as a valuable tool for simulating regional shifts in vegetation carbon sequestration dynamics is evident. In this study, we explore the constraints and prospects for carbon sequestration in these sensitive ecological areas by leveraging NPP analysis. A model to evaluate the relative contributions of climate change (CLC) and land use change (LUC) to carbon sequestration variability was developed, providing quantitative insight into their respective impacts within these zones. Our research revealed a significant upwards trend in NPP across the study area, with an annual increase of 3.73 gC·m-2 year-1. Notably, the Southwestern Karst Area and the Loess Plateau Area experienced the greatest increases, at rates of 9.68 gC·m-2 year-1 and 6.95 gC·m-2 year-1, respectively. This growth exhibited a geographical gradient that was more pronounced in the southeast and diminished toward the northwest, although the Northwest Arid Area was an exception, where the spatial trend of NPP primarily showed a downwards trajectory. This suggests resilience and the potential for enhanced carbon capture in these ecologically sensitive areas. This study identified CLC and LUC as key drivers of NPP increases, with their multiyear average impacts measured at 0.69 gC·m-2 year-1 and 1.03 gC·m-2 year-1, respectively, generally yielding positive effects. The impact varied across regions and land use scenarios. In areas experiencing land use changes, the positive and negative impacts of LUC on NPP were 32.47% and 22.68%, respectively, outpacing the effects of CLC. In contrast, in stable land use areas, the positive impact of CLC on NPP (26.65%) exceeded its negative effect (21.74%). Our work seeks to offer comprehensive insights into carbon sequestration capacities, elucidate multifactorial contributions, and develop targeted strategies to increase carbon sequestration in fragile ecosystems.