Clogging area is often formed around the prefabricated vertical drain during vacuuming preloading of waste mud. The accurate measurement and calculation of the permeability coefficient of mud in the clogging zone is critical to predict the consolidation of waste mud. Since it is difficult to measure the permeability coefficient of mud in the clogging zone directly and lack of theoretical derivation of permeability coefficient of clogging zone, a calculation method of the permeability coefficient and thickness of the clogging zone was proposed. A test device was established to investigate the formation of the clogging zone and validate the calculation method. The practicability and feasibility of the calculation method were proved by the test. It is concluded that the vacuum degree should be controlled below 90 kPa when vacuum preloading is conducted on the waste mud in practice, and the lower the vacuum degree used in the vacuum preloading between 60 kPa and 80 kPa, the slower the formation of the clogging zone is. The proposed permeability coefficient calculation method of the clogging zone can be used in consolidation function to predict the consolidation degree of mud in vacuum preloading process.