In this study, we investigated the effects of originating from cotton straw dissolved organic matter (CM) and farmyard manure dissolved organic matter (FM) on the physiological growth and Cd uptake and transport of cotton under two exogenous Cd addition gradients (5 mg·kg− 1 and 10 mg·kg− 1; 0 mg·kg− 1 as control) by pot experiments, and characterized the structures of CM and FM by UV-Visible spectroscopy. The results showed that CM had more low aromatic and low molecular weight hydrophibic fulvic acid fractions than FM. Cd stress reduced the total biomass (especially the lints), leaf photosynthetic intensity and SPAD value, increased the Cd content and transport coefficient in all parts of cotton, and stimulated the oxidative stress response in leaves. At low Cd levels (no exogenous Cd addition), application of DOM promoted cotton growth and increased leaf photosynthetic intensity and SPAD values; at medium to high Cd levels (5 mg·kg− 1 and 10 mg·kg− 1 exgenous Cd addition), application of DOM exhibited inhibitory effects on cotton growth (as shown by reduced leaf photosynthetic capacity, altered membrane antioxidant regulation) and changed Cd content in various parts of cotton. In addition, the inhibitory effect of CM on cotton growth and the ability to change Cd content in all parts was greater than that of FM. The redundancy analysis showed that the effect of DOM addition on cotton growth changed from promotion to inhibition when the level of exogenous Cd contamination reached 5 mg·kg− 1. Therefore, both straw return and farmyard manure application (especially straw return) in agricultural fields with high Cd contamination levels (≥ 5 mg·kg− 1) can be harmful to cotton physiological growth and pose a threat to cotton production.