Mass-extinction with instantaneous and short-term effects on extreme climate and deteriorated ocean environment across the Cretaceous/Paleogene boundary (K/PgB) has been verified by an array of geological records, however, a longer-term (~100−1000 Kyr) post-K/PgB variation remain poorly understood, particularly due to the scarcity of terrestrial records. This study presents carbon isotope analyses of pedogenic carbonates in the Nanxiong Basin, South China to reconstruct carbon cycles and atmospheric CO₂ concentrations (pCO₂) spanning 70.0–62.0 Ma. Combined with data from Songliao Basin (China) and Tornillo Basin (USA), δ¹³C displays a post-K/PgB (66.0-64.5 Ma) vibration that is correlative to the surface ocean but mirroring to the bottom ocean. The vibration shows a pattern of collapse and smooth towards rebound, constituting a process of ~400 Kyr (millennia) deterioration, ~300 Kyr stabilization and ~800 Kyr recovery for the longer-term ecosystem and environment. A similar pattern is observed for the reconstructed pCO₂, correlating to changes of sea surface temperature (SST) but contrasting bottom water temperature (BWT). With the discrepancy of longer-term proxy variations, it is proposed that ecosystems and environments in terrestrial and surface ocean had experienced a more unstable, difficult and erratic recovery process and were much more sensitive to climatic changes than in deep ocean for ~1.5 million years in the aftermath of the end-Cretaceous mass extinction. In addition, the decoupling of proxy variations from expected effects implies Deccan volcanism and Chicxulub impact may not have played a key role in the longer-term CO₂ perturbation and environmental change following the K/PgB.