The present invention relates to an on-line monitoring system for the clearance of the shaft system of a reciprocating rolling mill and a monitoring method thereof, which establishes a comparison table, retrieves a plurality of actual vibration signals of a shaft system of a rolling mill, and calculates the actual clearance of the shaft system of the rolling mill according to the actual vibration signals and the comparison table. The on-line monitoring system for the clearance of the shaft system of a reciprocating rolling mill and monitoring method thereof according to the present invention is carried out on the basis of impact vibration induced in a rolling process of the rolling mill for on-line inspection of the clearance dimension of the shaft system. Further, the on-line monitoring system for the clearance of the shaft system of a reciprocating rolling mill and monitoring method thereof according to the present invention provides real time information regarding the clearance of a rolling mill shaft system to a mill operator or maintenance personnel in order to determine if it conforms to the standards of control, so as to facilitate management of the clearance of a rolling mill and reduce impact vibration caused by the clearance of the shaft system during the rolling process, thereby extend the service life of the rolling mill.