In this paper, the notion of generalized Reynolds operators on Lie-Yamaguti algebras is introduced, and the cohomology of a generalized Reynolds operator is established. The formal deformations of a generalized Reynolds operator are studied using the first cohomology group. Then, we show that a Nijenhuis operator on a Lie-Yamaguti algebra gives rise to a representation of the deformed Lie-Yamaguti algebra and a 2-cocycle. Consequently, the identity map will be a generalized Reynolds operator on the deformed Lie-Yamaguti algebra. We also introduce the notion of a Reynolds operator on a Lie-Yamaguti algebra, which can serve as a special case of generalized Reynolds operators on Lie-Yamaguti algebras.