Phenology—mainly associated with climatic factors—is crucial for the accurate estimation of cumulative annual carbon exchange between terrestrial ecosystems and the atmosphere. However, the effects of changes in phenology on annual vegetation productivity and its regulatory mechanisms remain unclear, particularly in agricultural ecosystems. Therefore, in this study, we examined the associations among cumulative net ecosystem productivity (NEP), phenological metrics, and climatic factors based on long-term (2005–2014) eddy covariance flux and meteorological observations in a maize cropland in Northeast China. The results showed that carbon uptake period (CUP) was mainly determined by the end date of CUP (ECUP) in autumn. Cumulative NEP from May to September (NEP₅₋₉), a period generally corresponding to the growing season, significantly increased with NEP_max (defined in this study as the 90th percentile of daily NEP during CUP) and CUP. NEP_max explained greater interannual variation in NEP₅₋₉ than CUP. The start date of CUP (SCUP) and ECUP were both advanced with increasing winter temperature, but ECUP was more temperature-sensitive than SCUP. Thus, CUP tended to shorten with increasing temperature, ultimately decreasing cumulative NEP. In addition, NEP_max decreased with increasing precipitation in summer and autumn. The Greenup and MidGreendown dates from the MODIS Global Vegetation Phenology (MCD12Q2) product generally captured the interannual variation in the carbon flux-based SCUP and ECUP, respectively, well. The results of this study would be of great significance for predicting the response of ecosystem productivity to plant phenology shifts in agricultural ecosystems in future climate change scenarios.