Rising atmospheric CO2 levels, a significant consequence of anthropogenic activities, profoundly impact global agriculture and food security by altering plant physiological processes. Despite extensive research, a comprehensive understanding of the specific effects of elevated CO2 on maize (Zea mays L.)’s primary and secondary metabolism remains elusive. This study investigated the responses of maize seedlings cultivated in open-top chambers (OTCs) under three CO2 concentrations: ambient (380 ppm), elevated (600 ppm), and high (1800 ppm). Key growth parameters, including plant height, leaf area, and aboveground biomass (leaf and stem), were assessed alongside metabolic profiles encompassing nonstructural and structural carbohydrates, syringyl (S) and guaiacyl lignin, the syringyl-to-guaiacyl (S/G)-lignin ratio, photosynthetic pigments, total soluble protein, and malondialdehyde (MDA) levels. The results demonstrated that exposure to 600 ppm CO2 significantly enhanced plant height, leaf area, and aboveground biomass compared to ambient conditions. Concurrently, there were notable increases in the concentrations of primary metabolites. In contrast, exposure to 1800 ppm CO2 severely inhibited these growth parameters and induced reductions in secondary metabolites, such as chlorophyll and soluble proteins, throughout the growth stages. The findings underscore the intricate responses of maize metabolism to varying CO2 levels, highlighting adaptive strategies in primary and secondary metabolism under changing atmospheric conditions. This research contributes to a nuanced understanding of maize’s physiological adaptations to future climate scenarios characterized by elevated CO2, with implications for sustainable agriculture and food security.