Stable carbon isotope ratios (13C/12C) have been extensively used to trace carbon flow, and partition net ecosystem CO2 exchange. However, the CO2 isotopic data are still very limited in terrestrial ecosystems of maritime Antarctica. Here, we chose six tundra sites to investigate the isotopic compositions of CO2 during ecosystem respiration and photosynthesis, and the relationships with environmental variables using the static chamber method. For all tundra sites, ecosystem respirated-CO2 was 13C-depleted while vegetation photosynthesis resulted in the enrichment of 13C in the chamber headspace, compared with local atmospheric CO2. The δ13C-CO2 showed a strong negative correlation with CO2 concentrations in the chamber headspace both under dark condition (r2 = 0.70, p < 0.01) and under light condition (r2 = 0.29, p < 0.05), whereas δ18O-CO2 was almost stable, only with a small fluctuation from − 7.7 to − 8.3‰. The δ13C of ecosystem-respired (δr) and photoassimilated-CO2 (δp) fluctuated from − 12.4 to − 15.1‰ and − 10.5 to − 12.6‰, respectively, indicating that lower C isotopic discrimination occurred during plant photosynthesis and tundra ecosystem respiration, compared with reported data from other global ecosystems. Overall there was a small but distinct negative carbon isotopic disequilibrium (D: − 1 to − 3‰) between δr and δp at the spatial or summertime scale. The δp and δr showed consistent summertime variation patterns with significant positive correlation (r2 = 0.95, p < 0.01). The δr and δp significantly negatively correlated with respiration rates (r2 = 0.91, p < 0.01) and photosynthesis rates (r2 = 0.86, p < 0.01), respectively, and the δr, instead of δp, significantly correlated with net ecosystem exchange fluxes (r2 = 0.75, p = 0.012). The summertime patterns of δr, δp and D sensitively corresponded to changing temperature, precipitation and sunlight intensity, supporting the links between CO2 isotope fractionation and environmental variables during ecosystem respiration and plant photosynthesis. It was found that penguin activities had no significant effect on δr and δp although their activities significantly increased tundra ecosystem respiration and photosynthesis fluxes. The investigation of CO2 isotopic compositions contributes to better understanding of carbon cycling in maritime Antarctic tundra ecosystems.