During the formation and development of glacial meltwater runoff, hydrochemical erosion is abundant, especially the hydrolysis of K/Na feldspar and carbonates, which can consume H+ in the water, promote the formation of bicarbonate by dissolving atmospheric CO2, and affect the regional carbon cycle. From July 21, 2015, to July 18, 2017, the CO2 concentration and flux were observed by the eddy covariance (EC) method in the relatively flat and open moraine cover area of Koxkar Glacier in western Mt. Tianshan, China. We found that: (1) atmospheric CO2 fluxes ranged from − 408.95 to 81.58 mmol m−2 day−1 (average − 58.68 mmol m−2 day−1), suggesting that the study area is a significant carbon sink, (2) the CO2 flux footprint contribution areas were primarily within 150 m of the EC station, averaging total contribution rates of 93.30%, 91.39%, and 90.17% of the CO2 flux in the snow accumulation, snow melting, and glacial melting periods, respectively. Therefore, the contribution areas with significant influences on CO2 flux observed at EC stations were concentrated, demonstrating that grassland CO2 flux around the glaciers had little effect at the EC stations, (3) in the predominant wind direction, under stable daytime atmospheric stratification, the measurement of CO2 flux, as interpreted by the Agroscope Reckenholz Tanikon footprint tool, was 79.09% ± 1.84% in the contribution area. This was slightly more than seen at night, but significantly lower than the average under unstable atmospheric stratification across the three periods of interest (89%). The average distance of the farthest point of the flux footprint under steady state atmospheric conditions was 202.61 ± 69.33 m, markedly greater than that under non-steady state conditions (68.55 ± 10.34 m). This also indicates that the CO2 flux observed using EC was affected primarily by hydrochemical erosion reactions in the glacier area, (4) a good negative correlation was found between net glacier exchange (NGE) of CO2 and air temperature on precipitation-free days. Strong ice and snow ablation could promote hydrochemical reactions of soluble substances in the debris area and accelerated sinking of atmospheric CO2. Precipitation events might reduce snow and ice melting, driven by reduced regional temperatures. However, a connection between NGE and precipitation, when less than 8.8 mm per day, was not obvious. When precipitation was greater than 8.8 mm per day, NGE decreased with increasing precipitation, (5) graphically, the slope of NGE, related to daily runoff, followed a trend: snow melting period > snow accumulation period > early glacial ablation period > late glacier ablation period > dramatic glacier ablation period. The slope was relatively large during snow melting, likely because of CO2 sinking caused by water–rock interactions. The chemical reaction during elution in the snow layer might also promote atmospheric CO2 drawdown. At the same time, the damping effect of snow cover and the almost-closed glacier hydrographic channel inhibited the formation of regional runoff, possibly providing sufficient time for the chemical reaction, thus promoting further CO2 drawdown.