The invention discloses a method for designing the embedded depth of foundation of the transverse dentated sill based on the mud-rock flow soft ground energy dissipation and the application thereof. In the method, firstly, the energy consumption hi during the fall of mud-rock flow through the transverse dentated sill is calculated; subsequently, the critical longitudinal slope gradient of the initiation and deposit of the mud-rock flow i0 is calculated; subsequently, the energy consumption coefficient Phi when the mud-rock flow passes the transverse dentated sill and the scour depth below thesill Delta when the mud-rock flow passes the transverse dentated sill are calculated; and finally, the embedded depth of foundation H of the transverse dentated sill is calculated. The invention is applicable to the prevention and treatment of mud-rock flow with hyperconcentrated bi-phase two-dimensional flow, can form a drainage canal with a guide side wall or coordinate with a dam for sand collection to be used for prevention and treatment of the mud-rock flow. Compared with the prior art, on the basis of fully guaranteeing the secure operation of the transverse dentated sill, the method can reasonably confirm the embedded depth of foundation of the transverse dentated sill and save the project cost at utmost, thus being beneficial to the later operation management of the project, furthermore, the calculation method is effective, fast, easy and convenient, and meets the actual project requirement.