In the open-top chambers, the effects of different combinations of atmospheric CO₂ concentration ([CO₂]), nitrogen (N) and phosphorus (P) levels on cucumber were studied by the nutrient solution culture method, in terms of micronutrients concentrations and root morphological traits. Three [CO₂] levels (400 μmol/mol (CK, C1), 625 μmol/mol (C2), 1200 μmol/mol (C3)), three N levels (low N (N1), medium N (N2), high N (N3)) and two P levels (low P (P1), medium P (P2)) were used. The results showed that the N concentrations in all parts of cucumber increased with the increase of N level, and the N concentration in N3 treatment was significantly higher than that in N1 and N2. The increase of P level also promoted the N concentrations in cucumber. The concentrations of P in all parts of plants increased with the P supply increasing. Under the condition of N deficiency (N1), the concentration of P in each part increased. Elevated [CO₂] reduced N and P concentrations in specific parts of cucumber plants. The total root length and total root surface area of cucumber increased with the [CO₂] increasing. The concentration of calcium (Ca) in the roots of cucumber decreased significantly with the increase of [CO₂], whereas higher N and P levels significantly increased its concentration. There were apparent interactions between the [CO₂] and P level, N level and P level, and within these three factors on Ca concentration in the roots of cucumber. The rise of N level and P level also significantly increased the concentration of Ca in cucumber leaves and the concentration of magnesium (Mg) in stems, and there was a significant interaction between N and P levels. Under the condition of P deficiency (P1), the total root length and total root surface area increased with the increase of N level, whereas a decrease in P levels caused an increase in total root length and total root surface area at the same N level and [CO₂]. In general, the increase of [CO₂] can promote the growth of cucumber roots, but it will reduce the concentrations of mineral elements such as N, P, Ca and Mg in some parts of cucumber. However, the increase of N and P levels can promote the absorption of mineral nutrients in roots by enhancing the growth and vitality of cucumber, thereby alleviating the risk of a decrease in mineral elements concentrations due to the elevated [CO₂]. This suggests us that application of the suitable amount and the matched proportion of mineral elements are quite necessary while CO₂ fertilization is conducted to the greenhouse vegetables.