On-line monitoring of flow rate is rather important to evaluate the water consumption of the pump-turbine and the overall efficiency of the pumped storage station. Flow rate can be worked out based on the flow differential pressure measured in the flow passage and coefficients determined on model test. But the coefficients must be calibrated to obtain the reliable flow rate. As thermodynamic method is a common way to measure the discharge of prototype pump-turbine, site test is carried out on a vertical pump-turbine with 600 m rated head to calibrated the coefficients in this paper. Measuring devices are designed to satisfy both the turbine and pump operating conditions, and test results of flow rate at both turbine and pump operating conditions are presented and show that the calibrated coefficients are different to the predicted values. The calibrated results indicate the importance of site calibration on prototype turbine to ensure the monitoring validity on real-time flow rate.