Abstract: Phosphorus (P), the second important plant nutrient, regulates crop adaptation to climate change. The organic matter content of Mollisols in different areas of Northeast China is quite different, which greatly influences crop nutrient absorption. However, few studies have investigated the long-term effects of elevated CO₂ concentration on soybean growth, soil phosphorus fraction and relevant microbial mechanisms with different organic matter content of Mollisols. The study used open-top growth chambers to mainly investigate the effects of elevated CO₂ on soil phosphorus fractions and relevant functional genes in Mollisols with different organic matter content. The results showed that the response of P uptake of soybean to the long-term elevated CO₂ was the same change with different organic matter content, increasing first and then decreasing, while differences existed on P fractions in rhizosphere of soybean. Elevated CO₂ decreased NaHCO₃-P_o fraction in high-SOM (H-SOM) soil, however, elevated CO₂ favored the accumulation of organic fraction (NaHCO₃-P_o and NaOH-P_o), reduced inorganic fraction (NaOH-P_i) in low-SOM (L-SOM) soil. In addition, elevated CO₂ concentration increased the copy numbers of phoC by 53.0% in H-SOM, but increased the copy numbers of pstS by 44.4% in L-SOM. Therefore, under long-term climate change, soybean can meet the P demand through organic P mineralization by soil microorganisms in H-SOM, while inorganic P and relevant functional genes are affected in L-SOM.