The invention belongs to the technical field of construction site digital management and particularly relates to a construction site digital management system and an application method thereof. The management system comprises five sub systems, namely, a PLS (personnel location system), an access control system, a material management system, a shield operating system and a duct piece tracking system, wherein all the sub systems are connected with a remote database server, five sub database corresponding to the five sub systems are established in the remote database server, all the sub systems perform read-write operation on a main management object in a construction site range by using an RFID (radio frequency identification) technology, read data are uploaded to all corresponding sub databases in real time, and the operating authorization of a handheld RFID read head and the operating authorization of a shield machine are obtained through cross verification of data among all main sub databases. The management system and the application method have the advantages as follows: conventional extensive management is improved, the management responsibility is cleared, the management level is improved, and engineering information management, digital management and visual management are realized.