The properties of the heat source determine the exploitation potential and scientific research value of a high-temperature hydrothermal geothermal system. Existing hydrogeochemical and geophysical methods for discriminating heat sources have noticeable shortcomings, and an economic and universally applicable discrimination method is needed. In this study, three groups of typical geothermal waters from magmatic and non-magmatic geothermal systems in China were taken as the research objects. The Li concentrations of these geothermal waters were analyzed and the differences in their Li enrichment mechanisms were explored, while taking the cooling process of the geothermal water and the water–rock interactions into consideration. Finally, a more economical and universal new method for determining whether a hydrothermal geothermal system has a magmatic heat source based on the Li concentration was developed. The results show that: (1) the main ions in the magmatic geothermal waters were Na, HCO3, and Cl, but for the main ions in the non-magmatic geothermal waters were Na, Ca, and SO4. (2) Generally, the Li concentrations of the magmatic geothermal water samples were significantly higher than those of the non-magmatic geothermal water samples and most of the geothermal waters with a magmatic heat source were characterized by Li concentration of ≥5 mg/L and reservoir temperatures of ≥150 °C, while the geothermal waters with a non-magmatic heat source did not have this characteristic. (3) The magmatic geothermal waters mainly underwent the conductive and adiabatic cooling processes and also experienced cold-water mixing, whereas the non-magmatic geothermal waters mainly experienced cold-water mixing and conductive cooling. (4) Li-bearing mica was the main source of the Li from the host rocks and the amount of Li that removed by the adsorption of octahedral silicate minerals was greater in the magmatic geothermal systems than in the non-magmatic geothermal systems. (5) The additional amount of Li and heat provided by magmatic fluids were the key factors causing the Li enrichment, and the water–rock interactions between the geothermal waters and the host rocks were not sufficient to make the Li concentration of the geothermal waters reach 5 mg/L. (6) The Li concentration can be used universally to indicate the properties of the heat source of hydrothermal high-temperature geothermal system. In this study, a universal method for discriminating the heat sources of hydrothermal high-temperature geothermal systems based on the Li concentration was developed. Our findings provide a theoretical basis and effective method for evaluating types of geothermal resource and are of great significance for understanding the enrichment of lithium in geothermal water.