It has been conjectured that duality cascade occurs in the $mathcal{N}=3$ supersymmetric Yang-Mills Chern-Simons theory with the gauge group $U(N )_k times U(N+M )_{-k}$ coupled to two bi-fundamental hypermultiplets. The brane picture suggests that this duality cascade can be generalized to a class of 3d $mathcal{N}=3$ supersymmetric quiver gauge theories coming from so-called Hanany-Witten type brane configurations. In this paper we perform non-perturbative tests of the duality cascades using supersymmetry localization. We focus on $S^3$ partition functions and prove predictions from the duality cascades. We also discuss that our result can be applied to generate new dualities for more general theories which include less supersymmetric theories and theories without brane constructions.