This paper addresses the disturbance decoupling problem for large-scale Boolean networks. First, the original network is decomposed into several smaller subnetworks via a network aggregation approach, which significantly reduces computational complexity. Then, a state-flipping control strategy is applied to achieve disturbance decoupling within these subnetworks. Necessary and sufficient conditions are established under both uncontrolled and controlled scenarios, leading to the overall disturbance decoupling of the original large-scale Boolean network. Furthermore, this paper proposes two algorithms: One for verifying the feasibility of disturbance decoupling in the original network, and the other for finding the minimum set of flipped nodes required to achieve disturbance decoupling in each subnetwork. Finally, a numerical example illustrates the effectiveness of the proposed methodology.