Significant hydrogeochemical changes may occur prior- and post-earthquakes. The Xiaojiang fault zone (XJF), situated in a highly deformed area of the southeastern margin of the Tibetan Plateau, is one of the active seismic areas. In this study, major and trace elements, and hydrogen and oxygen isotopes of 28 sites in hot springs along the XJF were investigated from June 2015 to April 2019. The meteoric water acts as the primary water source of the hot spring in the XJF and recharged elevations ranged from 1.8 to 4.5 km. Most of the hot spring water in the study area was immature water and the water–rock reaction degree was weak. The temperature range was inferred from an equation based on the SiO2 concentration and chemical geothermal modeling: 24.3~96.0 °C. The circulation depth for the springs was estimated from 0.45 to 4.04 km. We speculated the meteoric water firstly infiltrated underground and became heated by heat sources, and later circulated to the earth’s surface along the fault and fracture and finally constituted hot spring recharge. Additionally, a continuous monitoring was conducted every three days in the Xundian hot spring since April 2019, and in Panxi and Qujiang hot springs since June 2019. There were short-term (4–35 d) seismic precursor anomalies of the hydrochemical compositions prior to the Xundian ML4.2, Dongchuan ML4.2, and Shuangbai ML5.1 earthquakes. The epicentral distance of anomalous sites ranged from 19.1 to 192.8 km. The anomalous amplitudes were all over 2 times the anomaly threshold. The concentrations of Na+, Cl−, and SO42− are sensitive to the increase of stress in the XJF. Modeling on hydrology cycles of hot springs can provide a plausible physicochemical basis to explain geochemical anomalies in water and the hydrogeochemical anomaly may be useful in future earthquake prediction research of the study area.