In order to exploit and protect the geothermal water scientifically, the chemistry and isotope of geothermal water are studied in Nanwenquan anticline. It is show that the geothermal water comes from atmosphere precipitation in the north of Tongluoxia anticline, in which the Tongluoxia anticline and Nanwenquan anticline are whole geothermal water system. The geothermal water flows from north to south. The geothermal water has hydraulic contact from north to south, from the western limb to eastern limb. The geothermal waters in Nanwenquan anticline are whole geothermal water system. Every exploration of the geothermal water in Nanwenquan anticline should layout. So it can avoid that the yield is higher than pondage, and the geothermal water source environment is destroyed. The study provides theoretical gist for exploiting and utilizing rationally and protecting geothermal water resource effectively.