<p>Carbon dynamics in alpine inland basins are jointly regulated by hydrothermal conditions, yet the elevational threshold at which hydrothermal drivers shift remains unquantified in the Qinghai Lake Basin. Using multi-source remote sensing data (2003–2023) with piecewise linear regression and structural equation modeling, we examined spatiotemporal patterns and drivers of gross primary productivity (GPP), net primary productivity (NPP), and carbon use efficiency (CUE) during the growing season. The results are as follows: (1) GPP and NPP were low in the northwest and high in the southeast, with multi-year means of 307.9 and 260.23 g C m⁻², respectively, both increasing significantly; (2) a clear ecological threshold at ~3526 m was detected (GPP, 3524.80 ± 7.11 m; NPP, 3527.38 ± 7.21 m), suggesting a shift in the relative importance of hydrothermal drivers across the identified elevation threshold, with productivity transitioning from primarily moisture-constrained to temperature-sensitive; (3) CUE regulation was decoupled from carbon fixation: normalized difference vegetation index (NDVI) had a negative effect (<i>β </i>= −0.28) above 3526 m, suggesting increased vegetation may reduce CUE via enhanced respiration; (4) zoning based on this threshold showed that high and medium carbon sequestration potential areas were almost entirely (&gt; 99%) above the threshold, whereas 99.6% of low-potential areas occurred below it, supporting differentiated basin management. This study quantifies a pivotal elevational threshold, reveals the decoupling between carbon fixation and utilization processes in response to shifts in hydrothermal drivers, and provides a practical framework for carbon cycle prediction and management in alpine inland basins.</p>