Abstract A new method for monitoring hydrothermal reactions on the millisecond time scale has been developed using a micro-tube flow reactor. The system was designed based on a high-pressure pump, a sample-loop injector, a narrow-bore size capillary, a cooling bath, back-pressure tubing, and a sampling port. Samples were analyzed using high-performance liquid chromatography. Kinetic analyses of the hydrolyses of adenosine 5′–triphosphate (ATP) and adenosine 5′–monophosphate (AMP) on the millisecond time range at 250—315 °C were demonstrated so as to evaluate the performance of the method. In conclusion, monitoring was successful for the hydrolysis of ATP and AMP in 2—50 ms using fused-silica capillary tubing with 0.015 and 0.025 mm inner diameter (ID). The method enables real-time monitoring of hydrothermal reactions in about 100-times shorter time range than other techniques. This paper proposes apparent rate constants and activation energy for the consecutive hydrolysis of ATP to adenine at high temperatures that were difficult to determine by a conventional batch method. On the basis of the rate constants, kinetics and mechanistic analyses of the step-wise decomposition of ATP were investigated from the viewpoint of the RNA world hypothesis under hydrothermal environments.