Background and Objectives: Deep seawater has been shown to restore pancreatic function in obese diabetic mice and considerably improve the homeostatic model assessment for insulin resistance, total cholesterol, and low-density lipoprotein cholesterol concentrations in patients with impaired fasting glucose or glucose tolerance. In this study, the effect of 12-week daily consumption of magnesium (Mg2+)-containing deep seawater mineral extracts on blood glucose concentration and insulin metabolism-associated indicators was investigated in patients with impaired glucose tolerance. Materials and methods: In this 12-week randomized, double-blind trial, patients (n = 37) with impaired glucose tolerance consumed deep seawater mineral extracts. Changes in blood glucose concentration and related indicators were compared between the treatment group and placebo group (n = 38). Results: The fasting insulin, C-peptide, homeostatic model assessment for insulin resistance, quantitative insulin sensitivity check index, homeostatic model assessment of beta-cell function, and Stumvoll insulin sensitivity index values in the deep seawater mineral extract group showed improvements compared with the placebo group. However, no significant differences between groups were observed in fasting blood glucose, postprandial blood glucose, glycated hemoglobin, or incremental area under the curve values. Conclusions: Oral supplementation with deep seawater mineral extracts enriched in Mg2+ markedly improves insulin sensitivity in patients with pre-diabetes. This study illustrates the potential clinical application of natural Mg2+ from deep seawater to alleviate insulin resistance in patients with pre-diabetes. Trial registration: This trial was retrospectively registered with Clinical Research information Service (CRIS), No. KCT0008695, on 8 August 2023.