The annual globally averaged atmospheric carbon dioxide concentration is expected to reach 550 ppm around 2050 unless measures are taken to mitigate its increase. Field experiments suggest that the nutrient contents of food crops are decreased substantially under elevated carbon dioxide conditions, which will lead to additional nutritional consequences on top of those related to the expected reductions of crop yield. Global modeling studies have suggested that such impacts would lead to a marked increase in the prevalence of nutrient deficiency. By using individual-level dietary survey data for Chinese adults, we conducted a comprehensive analysis on the nutritional consequence under the 550-ppm carbon dioxide scenario, with paying special attention to the distributional impact of nutrition degradation on different income groups. Our results suggest that the Chinese adult population would ingest around 2.17–4.75% less protein, iron, and zinc, and consequently, the prevalence of nutrient deficiency would increase by 1.35–4.42%. We also found a significant disparity in the nutrient loss rate and risk of deficiency among income groups: nutrient loss rates for the lowest-income group were 1.37–1.54 times greater than those for the highest-income group. Thus, the lowest-income group would experience a more considerable increase of nutrient deficiency risk under the 550-ppm carbon dioxide scenario. Moreover, we found that in the lower-income group nutrient intake for all three nutrients would be reduced simultaneously, which would leave this population more vulnerable to nutritional health risks. Our study revealed a marked inequality in the impact of the elevation of atmospheric carbon dioxide concentration. Nutrition intervention policies explicitly targeting affected populations must be explored to achieve social equality under elevated atmospheric carbon dioxide concentrations.