Learning the long-range interactions on large-scale mesh-based physical systems with flat Graph Neural Networks (GNNs) and stacking Message Passings (MPs) is challenging due to the scaling complexity w.r.t. the number of nodes and over-smoothing. Therefore, there has been growing interest in the community to introduce multi-scale structures to GNNs for physics simulation. However, current state-of-the-art methods are limited by their reliance on the labor-heavy drawing of coarser meshes or building coarser levels based on spatial proximity, which can introduce wrong edges across geometry boundaries. Inspired by the bipartite graph determination, we propose a novel pooling strategy, bi-stride to tackle the aforementioned limitations. Bi-stride pools nodes on every other frontier of the Breadth-First-Search (BFS), without the need for the manual drawing of coarser meshes and, avoid wrong edges introduced by spatial proximity. Additionally, it enables a reduced number of MP times on each level and the non-parametrized pooling and unpooling by interpolations, similar to convolutional Neural Networks (CNNs), which significantly reduces computational requirements. Experiments show that the proposed framework, BSMS-GNN, significantly outperforms existing methods in terms of both accuracy and computational efficiency in representative physics-based simulation scenarios.