The water cushion depth of stilling basin with shallow-water cushion is a key factor that affects the flow regime of hydraulic jump in the basin. However, the specific depth at which the water cushion is considered as “shallow” has not be stated clearly for now, and only conceptual description is provided. This paper attempts to specify the best water cushion depth based on the flow regime of hydraulic jump and underflow speed; namely, in case of critical hydraulic jump in the basin, the best water cushion depth is located where the minimum distance to the bottom plate of the stilling basin is 1/5~1/4 of the water cushion depth. The theoretical analysis indicates, at different inclinations of discharge chute (θ) and depth ratios of inlet (m), instead of monotonic change, the Froude number (Fr) at inlet of the stilling basin with shallow-water cushion firstly reduces and then increases as the flow velocity at discharge chute inlet (V) increases; the parameters of inflection point (critical flow velocity and critical Fr) increase as the inclinations of discharge chute (θ) and depth ratios of inlet (m) increase. Such regularity is the theoretical basis for selecting representative study cases. The reliability of the large eddy simulation calculation results are verified by a model test; in the paper, 30 cases including five different Froude numbers and six shallow-water cushion depths are selected, for calculating the hydraulic factors such as flow profile, flow regime and flow velocity in the stilling basin with shallow-water cushion; and the varying pattern between the best depth of stilling basin with shallow-water cushion (depth-to-length ratio) and the inflow Froude number is obtained which indicates that the best depth of stilling basin with shallow-water cushion varies little as the change of the Froude number before reaching the critical Froude number; however, the best depth-to-length ratio of stilling basin with shallow-water cushion increases as the Froude number increases after the critical Froude number is reached. The study results in this paper are of reference significance to design and calculation of the stilling basin with shallow-water cushion.