Graph neural networks are a promising architecture for learning and inference with graph-structured data. Yet, how to generate informative, fixed dimensional features for graphs with varying size and topology can still be challenging. Typically, this is achieved through graph-pooling, which summarizes a graph by compressing all its nodes into a single vector. Is such a “collapsing-style” graph-pooling the only choice for graph classification? From complex system’s point of view, properties of a complex system arise largely from the interaction among its components. Therefore, we speculate that preserving the interacting relation between parts, instead of pooling them together, could benefit system level prediction. To verify this, we propose SLIM, a graph neural network model for Structural Landmarking and Interaction Modelling. The main idea is to compute a set of end-to-end optimizable sub-structure landmarks, so that any input graph can be projected onto these (spatially) local structural representatives for a faithful, global characterization. By doing so, explicit interaction between component parts of a graph can be leveraged directly in generating discriminative graph representation. Encouraging results are observed on benchmark datasets for graph classification, demonstrating the value of interaction modelling in the design of graph neural networks.