Operational amplifier is a basic component for analog circuit design. The compensation network of an operational amplifier is crucial to improve the stability of the operational amplifier. In this paper, we present an automated compensation scheme design approach for operational amplifiers. We map the behavioral-level description of the operational amplifier to an acyclic graph and transfer the compensation design problem into a topology optimization problem. A feature mapping method is proposed to encode the graph and a bi-level Bayesian optimization approach is proposed to efficiently solve the topology optimization problem. Experimental results show that our proposed method can obtain competitive three-stage operational amplifiers compared to manual designs.