Abstract: Soil carbon fluxes exhibit substantial spatial heterogeneity, yet this variability is typically assessed across contrasting ecosystems. Fine-scale fluxes heterogeneity within ecosystems remains largely unaccounted for, which may bias regional carbon budget estimates. Here we present two-year in situ measurements of soil CO₂ and CH₄ fluxes across six representative patch types within three alpine ecosystems on the Tibetan Plateau (i.e., healthy and degraded patches in mesic meadows, tussocks and pools in wet meadows, and hollows and hummocks in wetlands). We quantify within-ecosystem patch variability in carbon fluxes and examine its effects on landscape-scale flux variation and inferred drivers. Our results showed that patches significantly affected soil carbon fluxes within ecosystems, with effect sizes that varied across ecosystem types and seasons. In mesic meadows, the variation of soil carbon fluxes between degraded and healthy patches were most pronounced during the non-growing season, with CH₄ fluxes differing by up to 88%. In wet meadows and wetlands, larger differences in soil carbon fluxes occurred during the growing season, with tussock-pool contrasts reaching 142% for CH₄ fluxes and hollow–hummock contrasts reaching 250% for CO₂ and 191% for CH₄ fluxes. Furthermore, incorporating patch variation increased landscape-scale CH₄ variability and changed the regulating drivers, weakening the influence of microclimates while strengthening the roles of soil properties (for CO₂) and microbial and soil factors (for CH₄). These findings identify within-ecosystem patches as a critical yet overlooked driver of soil carbon fluxes heterogeneity, underscoring the need to incorporate fine-scale variation into predictions of regional carbon cycling.

Key words: Spatial heterogeneity, carbon dioxide emission, methane flux,microtopography, Tibetan Plateau