Although the metabolism of phytochelatins and higher polyamines are linked with each other, the direct relationship between them under heavy metal stress has not yet been clarified. Two approaches were used to reveal the influence of polyamine content on cadmium stress responses, particularly with regard to phytochelatin synthesis: putrescine pre-treatment of rice plants followed by cadmium stress, and treatment with the putrescine synthesis inhibitor, 2-(difluoromethyl)ornithine combined with cadmium treatment. The results indicated that putrescine pre-treatment enhanced the adverse effect of cadmium, while the application of 2-(difluoromethyl)ornithine reduced it to a certain extent. These differences were associated with increased polyamine content, more intensive polyamine metabolism, but decreased thiol and phytochelatin contents. The gene expression level and enzyme activity of phytochelatin synthase also decreased in rice treated with putrescine prior to cadmium stress, compared to cadmium treatment alone. In contrast, the inhibition of putrescine synthesis during cadmium treatment resulted in higher gene expression level of phytochelatin synthase. The results suggest that polyamines may have a substantial influence on phytochelatin synthesis at several levels under cadmium stress in rice.