Accurate estimation of regional-scale terrestrial carbon budgets is of great importance but remains challenging. With particular advantages, the Long Short-Term Memory (LSTM) networks method show potential in improving regional carbon budget upscaling estimations. Here, based on LSTM, we upscale regional net ecosystem carbon exchange (NEE) with available flux tower measurements and satellite land surface observations in North America. With well-established ecosystem-specific LSTMs, we produced monthly NEE at a spatial resolution of 0.1°×0.1° over 2001–2021 (labeled as CROSS2023). Our estimate pointed the largest carbon sink to the Midwest Corn-Belt area during peak growing seasons and to the Southeast on an annual basis, agreeing with empirical knowledges. Moreover, the estimated seasonal variations of NEE by CROSS2023 coincided well with those by atmospheric inversions, i.e., the ensemble mean of Orbiting Carbon Observatory-2 Model Intercomparison Project (OCO-2 v10 MIP; r = 0.95, p < 0.001) and CarbonTracker2022 (CT2022) (r = 0.97, p < 0.001). The mean annual NEE was estimated at -1.27 ± 0.12 Pg C yr-1, aligning more closely with the inversions (-0.70 to -0.63 Pg C yr-1) than with existing upscaling estimates (-3.30 to -1.81 Pg C yr-1). In addition, our estimate plausibly captured the NEE spatial anomalies caused by all the recent extreme drought and flood events. We further confirmed that considering memory effects was critical for better indicating interannual variability and spatial anomalies of NEE induced by climate extremes. This study provides an improved bottom-up estimation of North American NEE, largely narrowing the gap with top-down inversions.