The phenological cycles of terrestrial ecosystems have shifted with the changing climate, and the altered timings of biogeochemical fluxes may also exert feedback on the climate system. As regulators of land carbon balance, relative shifts in photosynthetic and respiratory phenology under climate change are of great importance. However, the relative seasonal dynamics of these individual processes and their sensitivity to climate factors as well as the implications for carbon cycling are not well understood. In this study, we examined the relationship in the seasonality of gross primary production (GPP) and ecosystem respiration (RE) as well as their temperature sensitivities and the implications for carbon uptake with around 1500 site-years’ of data from FLUXNET 2015 and Boreal Ecosystem Productivity Simulator (BEPS) at 212 sites. The results showed that RE started earlier in the spring and ended later in the autumn than GPP over most biomes. Furthermore, the flux phenology metrics responded differently to temperature: GPP phenology was more sensitive to changes during the spring temperature than RE phenology, and less sensitive to autumn temperature than RE. We found large BEPS-observation discrepancies in seasonality metrics and their apparent temperature sensitivity. The site-based BEPS projections did not capture the observed seasonal metrics and temperature sensitivities in either GPP or RE seasonality metrics. Improved understanding of the asynchrony of GPP and RE as well as different sensitivity of environmental factors are of great significance for reliable future carbon balance projections.