Uchino initiated the investigation of twisted Rota-Baxter operators on associative algebras. Relevant studies have been extensive in recent times. In this paper, we introduce the notion of a twisted Rota-Baxter operator on a Hom-Lie algebra. By utilizing higher derived brackets, we establish an explicit $L_{\mathrm{\infty }}$-algebra whose Maurer-Cartan elements are precisely twisted Rota-Baxter operators on Hom-Lie algebra s. Additionally, we employ Getzler's technique of twisting $L_{\mathrm{\infty }}$-algebras to establish the cohomology of twisted Rota-Baxter operators. We demonstrate that this cohomology can be regarded as the Chevalley-Eilenberg cohomology of a specific Hom-Lie algebra with coefficients in an appropriate representation. Finally, we study the linear and formal deformations of twisted Rota-Baxter operators by using the cohomology defined above. We also show that the rigidity of a twisted Rota-Baxter operator can be derived from Nijenhuis elements associated with a Hom-Lie algebra.