The reasons for covariations of speleothem δ13C and δ18O remain controversial, primarily due to the limited high‐resolution stalagmite records that can be compared with meteorological data. This study presents δ13C and δ18O records of two coeval, annually laminated stalagmites (TS9701 and TS9501) spanning the past ∼2000 years from Shihua cave, Beijing, northern China. The low correlation between stalagmite TS9701 records, with annual resolution, and local annual precipitation as well as mean annual temperature on interannual to decadal scales indicates that the positive covariations of δ18O and δ13C in TS9701 are partly attributed to kinetic isotope effects caused by rapid CO2degassing. Isotopic disequilibrium between HCO3−(aq)and drip water, induced by prior calcite precipitation on cave ceiling and stalactite surface, is another potential contributing factor. δ18O and δ13C exhibits distinct patterns on multidecadal to millennial timescales. δ18O records show notable centennial variability, aligning with El Niño‐Southern Oscillation cycles. In contrast, δ13C profiles reveal a decreasing trend during the first ∼750 years, followed by an increasing trend. Prior to 1588 AD, variations in δ13C broadly correspond to changes in warm season temperature and/or moisture on centennial scale. Both δ13C records show an abrupt enrichment between 1588 and 1654 AD. Historical documents indicate that this anomaly is likely attributed to coal mining and resultant deforestation around Shihua cave during late‐Ming and early‐Qing Dynasties. In summary, while isotopic disequilibrium can cause high‐frequency covariations of speleothem δ18O and δ13C, it does not erase the imprints of climate changes and human activities on multidecadal to millennial timescales. This study examines the relationship between δ13C and δ18O of stalagmites from Beijing, northern China. We analyzed two stalagmites, TS9701 and TS9501, which grew over the past ∼2000 years. We found that the covariations in δ13C and δ18O on interannual to decadal scales do not directly correspond to local annual rainfall or temperature changes. Instead, these variations are partly caused by isotopic disequilibrium due to prior calcite precipitation on the cave ceiling and stalactite surface as well as rapid CO2degassing during stalagmite grew. However, δ18O and δ13C exhibit distinct patterns on multidecadal to millennial timescales. δ18O records show significant centennial variability, linked to El Niño‐Southern Oscillation cycles. δ13C records reveal a decreasing trend during the first ∼750 years, followed by an increasing trend. Before 1588 AD, variations in δ13C broadly matched changes in warm season temperature and/or moisture on centennial scale. Between 1588 and 1654 AD, δ13C records show a sudden increase, likely due to coal mining and the resulting deforestation around the cave during late‐Ming and early‐Qing Dynasties. In summary, while isotopic disequilibrium can cause high‐frequency variations in stalagmite isotopes, it does not erase the effects of climate changes and human activities over longer timescales. Correlation between δ18O and δ13C in a laminated stalagmite from northern China varies across multi‐timescalesInterannual to decadal covariations of stalagmite δ18O and δ13C partly result from isotopic disequilibrium as prior loss of 12C16O2Isotopic disequilibrium does not alter multidecadal to millennial isotopic variations in response to climate changes and human activities Correlation between δ18O and δ13C in a laminated stalagmite from northern China varies across multi‐timescales Interannual to decadal covariations of stalagmite δ18O and δ13C partly result from isotopic disequilibrium as prior loss of 12C16O2 Isotopic disequilibrium does not alter multidecadal to millennial isotopic variations in response to climate changes and human activities