[Objective] The study aims to analyze the metabolomic differences of potato roots to NaHCO3 stress, reveal the metabolic molecular mechanism of different potato varieties in response to NaHCO3 stress, and provide theoretical basis for optimizing potato breeding, cultivation techniques and production applications. [Methods] The root system of potato ‘V7’ and ‘KANG Nibeike’ seedlings was selected as the research object, and NaHCO3 solution was used to simulate alkali stress with different concentration gradients (CK, 10 mmol/L, 20 mmol/L, 30 mmol/L, 40 mmol/L, 50 mmol/L). The root metabolites of two potato varieties were analyzed by high performance liquid chromatography (LC-MS) and multidimensional statistics combined with non-targeted metabolomics detection. [Results] (1) Under NaHCO3 stress, 160 metabolites were up-regulated and 91 metabolites were down-regulated in ‘V7’ roots, 125 metabolites were up-regulated and 52 metabolites were down-regulated in ‘KANG Nibeike’ roots. (2) KEGG pathway enrichment analysis showed that 10 differential metabolic pathways were selected for each of the two varieties, among which 4 differential metabolic pathways, namely, biosynthesis of plant secondary metabolites, biosynthesis of unsaturated fatty acids, synthesis of histidine and purine-derived alkaloids, and pyrimidine metabolism, were the key metabolic pathways in response to alkali stress in potato roots. (3) Differential metabolites such as carbohydrates, amides, amines, oxy-containing organic compounds, alkaloids, phenolic acids, somatogenin, etc. are involved in the complex regulatory network of potato response to NaHCO3 stress. [Conclusion] The key metabolites and metabolic pathways of potato root in response to NaHCO3 stress were screened out. There were differences in the root metabolomics of alkaline tolerant cultivar ‘V7’ and alkali sensitive cultivar ‘KANG Nibeike’. At the same time, there were differences between the root metabolism of the same variety and CK under different stress levels. The accumulation of amino acids and their derivatives, organic acids and allantoin is an important characteristic of ‘V7’ root metabolism, which is more active and alkaline resistant than ‘KANG Nibeike’.