High time-resolution auto-monitoring techniques were used to obtain the data for TOC and hydrogeochemistry of groundwater, and air temperature and precipitation from August 2014 to September 2015 in Xueyu Cave karst watershed, Southwest China, and then the principal component regression model was used to reveal the variation of TOC in groundwater and its influencing factors. The results indicated that there were significant variations of the TOC and hydrogeochemistry of groundwater in seasonal timescale. The temperature and specific conductance (SpC) of groundwater showed higher values in summer and lower values in winter; while an opposite variation pattern for pH in groundwater was observed, and the TOC and turbidity of groundwater showed higher values in winter and summer seasons and lower values in spring and autumn seasons. Meanwhile, high time-resolution data revealed that the TOC of groundwater responded quickly to rainfall events with different intensities. Generally, an increasing trend for TOC in groundwater was observed during raining and a decreasing trend for TOC in groundwater was shown after rainfall events, especially after storm events due to the dilution effect of rainfall. The export and variations of the TOC in groundwater were mainly controlled by the precipitation and discharge of underground river in the study area, as revealed by the principal component regression model. The TOC increased with the increase of the precipitation, discharge and turbidity of groundwater, and declined with the increase of air temperature and pH of groundwater.