Li River appeared successively three times floods during May 8-17, 2012. We were high-frequency monitoring during the flood once every hour, real time monitoring the pH value, water temperature, EC(electrical conductivity), pCO2(carbon dioxide partial pressure), HCO3- and flow rate, analyzing karst carbon sinks dynamic changes during the flood. It was found that river hydrochemistry and karst carbon sinks in different stages with different variations in Li River. These floods were divided into 5 stages to discuss, researches have shown: AtIand Vstage the river hydrochemistry is not subjected to flooding, pCO2 and pH value, water temperature has distinct characteristics of diurnal variation. EC, flow rate and HCO3- is relatively stable; II, III and IV stage appear different changes characteristics are due to effects of flood, flow rate and HCO3- have a positive correlation at IV stage, with opposite of stage II and III stage. We use water chemistry-runoff method to calculate the amount of carbon sinks in the flood, found in the flood related coefficients between carbon sink and HCO3-, flow rate respectively 0.87 and 0.33. The carbon sink is 3491.06 t C during the flood monitoring, in which carbon sink at IVstage in flood are 4.52 times prior to the flood, which account for that carbon sink in the flood is much larger than the front of flood.