Realization of robust transmission and transformation of entangled states with high fidelity is crucial for the applications in quantum information, computing, and communications. However, it is hard to achieve currently because of scattering loss and disorder. Here, an inverse-design scheme is theoretically proposed and experimentally demonstrated to realize nearly perfect transmission and transformation of entangled photon states. The scheme is based on the determination of the transmission and transformation properties of entangled states, which depends on the overlap integrals among the initial states, eigenmodes of the system and target states. Thus, topologically protected channels are designed according to the requirements for the overlap integrals of these states. As a result, robust transmission and transformation of entangled states are achieved with high fidelity. The proposed scheme has been demonstrated experimentally using the constructed quantum walk platform. This work interconnects topology, quantum physics, and inverse design, and opens up a new avenue for quantum engineering.