Elevated atmospheric CO2 concentration (eCO2) exerts significant influence on nutrient requirement in plant. The investigation of C:N:P ratios in major cropping soils is important for managing nutrient balance and maximizing their use efficiency in future farming systems. This study aimed to examine the effect of eCO2 on the C:N:P ratios in different plant parts among soybean cultivars. Twenty-four soybean cultivars were planted in open top chambers at two CO2 concentrations (390 and 550 ppm) and sampled at the initial pod filling stage (R5) and the full maturity stage (R8). The C, N and P concentrations in root, stem, leaf and seed were determined. Elevated CO2 decreased the N concentrations in stem (-5.1%) and leaf (-3.2%) at R5, and in root (-24%), stem (-25%) and seed (-6.2%) at R8, resulting in a significant decrease of C:N ratio in the corresponding parts. The P concentration was significantly increased in root (6.0%), stem (7.9%) and leaf (16%) at R5, and in root (2.6%), stem (29%) and seed (16%) at R8 across 24 cultivars, leading to a decrease in the C:P ratio. Elevated CO2 significantly decreased the N:P ratio in root (-4.5%), stem (-12%) and leaf (-17%) at R5, and in root (-26%), stem (-57%) and seed (-22%) at R8. Furthermore, the response of C:N:P ratios to eCO2 varied greatly among soybean cultivars leading to significant CO2 × cultivar interactions. Nitrogen, but not P was the limiting factor for the soybean plants grown in Mollisols under eCO2. The considerable variation in the C:N:P ratios among cultivars in response to eCO2 indicates a potential improvement in soybean adaptability to climate change via selection new cultivars. Cultivars SN22 and ZH4 that did not considerably altered the C:N and C:P ratios in response to eCO2 are likely the optimal genomes in soybean breeding programs for eCO2 adaption.