Recently, new classes of infinite-dimensional algebras, quiver Yangian (QY) and shifted QY, were introduced, and they act on BPS states for non-compact toric Calabi-Yau threefolds. In particular, shifted QY acts on general subcrystals of the original BPS crystal. A trigonometric deformation called quiver quantum toroidal algebra (QQTA) was also proposed and shown to act on the same BPS crystal. Unlike QY, QQTA has a formal Hopf superalgebra structure which is useful in deriving representations.In this paper, we define the shifted QQTA and study a class of their representations. We define 1d and 2d subcrystals of the original 3d crystal by removing a few arrows from the original quiver diagram and show how the shifted QQTA acts on them. We construct the 2d crystal representations from the 1d crystal representations by utilizing a generalized coproduct acting on different shifted QQTAs. We provide a detailed derivation of subcrystal representations of C 3 , C 3 /Z n (n ≥ 2), conifold, suspended pinch point, and C 3 /(Z 2 × Z 2 ).