The invention provides a wireless beacon positioning system and a positioning method thereof, and belongs to the technical field of the internet of things. The system comprises a wireless beacon, an identification card and a positioning substation, wherein the wireless beacon and the positioning substation are paired and grouped by adopting an on-demand distribution way, and only the wireless beacon and the positioning substation in the same group can perform data communication; the wireless beacon performs time synchronization by adopting a dynamic on-demand time service principle, and the problem that the wireless beacon still can realize the on-demand group dynamic time service under the condition that the battery power supply is dormant as required is solved, through the emission fieldintensity, the attenuation coefficient on-demand configuration, signal intensity threshold filtering and like technology, the flexible requirements on the positioning precision on-demand deployment at the petrochemical, chemical engineering and like job fields are satisfies, the low cost and high-precision positioning effect is realized.