Taking melon cultivar 'Xiyu No. 1 ' as test material, a hydroponic experiment was conducted to investigate the effects of exogenous gamma-aminobutyric acid (GABA) on the seedlings polyamine metabolism under hypoxia stress. Compared with the control in normoxic treatment, the seedlings under hypoxia stress had significantly higher glutamic acid decarboxylase (GAD) activity and GABA content, and their polyamine synthesis enzymes activities all enhanced significantly, which led to a marked increase of polyamines contents. Meanwhile, the seedlings leaf- and root diamine oxidase (DAO) and polyamine oxidase (PAO) activities also had a significant increase. The increment of root arginine decarboxylase (ADC) activity was higher, which induced a higher content of free putrescine (Put) in roots, while the increment of leaf ornithine decarboxylase (ODC) and S-adenosylmethionine decarboxylase (SAMDC) activities were higher, inducing a higher content of free spermidine (Spd) in leaves. The PBs-extractable DAO and PAO activies in roots were significantly lower than those in leaves, but the cell wall-bound PAO activity was in adverse. Under hypoxia stress, the addition of exogenous GABA increased the leaf- and root GABA and glutamic acid contents and decreased the GAD activity significantly. The increase of arginine, ornithine, and methionine contents promoted the activities of polyamines synthesis enzymes, which led to the significant increase of polyamines contents and the significant decrease of DAO and PAO activities.