Graph neural networks (GNNs) are processing architectures that exploit graph structural information to model representations from network data. Despite their success, GNNs suffer from sub-optimal generalization performance given limited training data, referred to as over-fitting. This paper proposes Topology Adaptive Edge Dropping (TADropEdge) method as an adaptive data augmentation technique to improve generalization performance and learn robust GNN models. We start by explicitly analyzing how random edge dropping increases the data diversity during training, while indicating i.i.d. edge dropping does not account for graph structural information and could result in noisy augmented data degrading performance. To overcome this issue, we consider graph connectivity as the key property that captures graph topology. TADropEdge incorporates this factor into random edge dropping such that the edge-dropped subgraphs maintain similar topology as the underlying graph, yielding more satisfactory data augmentation. In particular, TADropEdge first leverages the graph spectrum to assign proper weights to graph edges, which represent their criticality for establishing the graph connectivity. It then normalizes the edge weights and drops graph edges adaptively based on their normalized weights. Besides improving generalization performance, TADropEdge reduces variance for efficient training and can be applied as a generic method modular to different GNN models. Intensive experiments on real-life and synthetic datasets corroborate theory and verify the effectiveness of the proposed method.