Small watersheds are fundamental units for natural processes and social management in Southwestern China. Accurately assessing carbon sinks in small watersheds is crucial for formulating carbon sink management policies. However, there has been a lack of assessment of the dynamics of carbon fluxes in the major ecosystems of small watersheds. Here, we selected the Reshuihe River watershed, which is a typical small watershed in Southwestern China, to measure carbon fluxes using eddy covariance systems for two years (October 2021 to September 2023) from three major ecosystems, namely forest, cropland, and non-timber forest. We compared variations and controlling factors of net ecosystem exchange (NEE), gross primary productivity (GPP), and ecosystem respiration (Re) among different ecosystems, and estimated annual watershed carbon flux based on the land cover areas of the three ecosystems. This study found that three ecosystems were net annual carbon sinks during the study period. Forest was the strongest (−592.8 and −488.1 gC m⁻² a⁻¹), followed by non-timber forest (−371.0 gC m⁻² a⁻¹), and cropland was the smallest (−92.5 and −71.6 gC m⁻² a⁻¹), after taking fallow period into account. Weeds were a significant source of carbon flux in non-timber forest ecosystems. It was also found that variations in daily NEE were controlled by photosynthetically active radiation and soil volumetric water content, with weak effects related to temperature also being observed. However, when the temperature exceeded 21 °C, GPP and Re were significantly reduced in cropland. Finally, it was discovered that the total carbon sink of the three ecosystems in the watershed for one year was −52.15 Gg C. Overall, we found that small watersheds dominated by forest ecosystems in Southwestern China have a strong carbon sink capacity.