Understanding feedbacks of ecosystem carbon sequestration to climate change is an urgent step in developing future ecosystem models. Using 187 site-years of flux data observed at 24 sites covering three plant functional types (i.e. evergreen forests (EF), deciduous forests (DF) and non-forest ecosystems (NF) (e.g., crop, grassland, wetland)) in North America, we present an analysis of both interannual and spatial relationships between annual net ecosystem production (NEP) and phenological indicators, including the flux-based carbon uptake period (CUP) and its transitions, degree-day-derived growing season length (GSL), and spring and autumn temperatures. Diverse responses were acquired between annul NEP and these indicators across PFTs. Forest ecosystems showed consistent patterns and sensitivities in the responses of annual NEP to CUP and its transitions both interannually and spatially. The NF ecosystems, on the contrary, exhibited different trends between interannual and spatial relationships. The impact of CUP onset on annual NEP in NF ecosystems was interannually negative but spatially positive. Generally, the GSL was observed to be a likely good indicator of annual NEP for all PFTs both interannually and spatially, although with relatively moderate correlations in NF sites. Both spring and autumn temperatures were positively correlated with annual NEP across sites while this potential was greatly reduced temporally with only negative impacts of autumn temperature on annual NEP in DF sites. Our analysis showed that DF ecosystems have the highest efficiency in accumulating NEP from warmer spring temperature and prolonged GSL, suggesting that future climate warming will favor deciduous species over evergreen species, and supporting the earlier observation that ecosystems with the greatest net carbon uptake have the longest GSL.