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In order to conduct a comprehensive study on the influence of cotton root growth and metabolic activity under cadmium stresses, we have conducted the transcriptome sequencing for cotton root that it processed under three different cadmium concentrations.The comparison results showed the expression level of thousand genes exhibited significant difference in root tissues.These genes are roughly clustered in thirteen classes, including cytoskeletal protein and the enzyme involved in cytoskeleton assembly and cytoskeleton depolymerization, transport protein (for example, sulfate transport protein, solute carrier family protein, dicarboxylic acid transport protein), photoresponse protein and the enzyme associated with polypeptide metabolic pathways.The cadmium stress mainly affects the transport system of root organization, and leads to accumulation of harmful metabolites, causes various stress, such as oxidative stress and osmotic pressure.In metabolic processes aspects, the metabolism of nitrogen-containing compounds, the synthesis of phenylpropanoids, and the synthesis of ketonic acid are three major biological processes that have major impacts on cadmium stress, these three biological processes are closely related with the synthesis and transport of plant hormones.Therefore, we believe that cadmium stress mainly affects the development of cotton roots from three aspects, including the root cell division, the absorption and transport of nutrient and plant hormone synthesis and transport.