Let $(L, alpha)$ be a Hom-Lie-Yamaguti superalgebra. We first introduce the representation and cohomology theory of Hom-Lie-Yamaguti superalgebras. Furthermore, we introduce the notions of generalized derivations and representations of $(L, alpha)$ and present some properties. Finally, we investigate the deformations of $(L, alpha)$ by choosing some suitable cohomology.