Despite extensive research on soil microbial carbon use efficiency (CUE), its linkage to actual soil organic C dynamics remains ambiguous. A key uncertainty is that CUE estimates derived from short-term labeling incubations assume a linear negative relationship with pulse respiration rates, thereby overlooking widespread nonlinear interactions and long-term microbial acclimation in natural ecosystems. Here, we synthesized 1,094 paired observations of CUE and average annual heterotrophic respiration rate (Rh) across global natural ecosystems, and found a nonlinear relationship between them governed by ecosystem productivity. In low-productive arid and cold regions, CUE declined with increasing Rh. In contrast, in high-productivity tropical and temperate regions, CUE stabilized at a low level (0.27±0.11) as Rh exceeded a threshold of 340±10.8 g C m-2 y-1. This shift reflects a fundamental microbial trade-off between C assimilation and the maintenance of stoichiometric homeostasis.