In this article we use the philosophy in [OS22] to construct the quantum difference equation of affine type $A$ quiver varieties in terms of the quantum toroidal algebra $U_{q,t}(\hat{\hat{\mathfrak{sl}}}_{r})$. In the construction, and we define the set of wall for each quiver varieties by the action of the universal $R$-matrix, which is shown to be almost equivalent to that of the $K$-theoretic stable envelope on each interval in $H^2(X,\mathbb{Q})$. We also give the examples of the instanton moduli space $M(n,r)$ and the Hilbert scheme $\text{Hilb}_{n}(\widehat{\mathbb{C}^2/\mathbb{Z}_{r}})$ to show the explicit form of the quantum difference operator.Comment: 59 page
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