Soil water deficit and salt stress are major limiting factors of plant growth and agricultural productivity. The primary root is the first organ to perceive the stress signals for drought and salt stress. In this study, maize plant subjected to drought, salt and combined stresses displayed a significantly reduced primary root length relative to the control plants. GC-MS was used to determine changes in the metabolites of the primary root of maize in response to salt, drought and combined stresses. A total of 86 metabolites were measured, including 29 amino acids and amines, 21 organic acids, four fatty acids, six phosphoric acids, 10 sugars, 10 polyols, and six others. Among these, 53 metabolites with a significant change under different stresses were identified in the primary root, and the content of most metabolites showed down-accumulation. A total of four and 18 metabolites showed significant up- and down-accumulation to all three treatments, respectively. The levels of several compatible solutes, including sugars and polyols, were increased to help maintain the osmotic balance. The levels of metabolites involved in the TCA cycle, including citric acid, ketoglutaric acid, fumaric acid, and malic acid, were reduced in the primary root. The contents of metabolites in the shikimate pathway, such as quinic acid and shikimic acid, were significantly decreased. This study reveals the complex metabolic responses of the primary root to combined drought and salt stresses and extends our understanding of the mechanisms involved in root responses to abiotic tolerance in maize.