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Abstract Spinodoid architected materials have drawn significant attention due to their unique nature in stochasticity, aperiodicity, and bi-continuity. Compared to classic periodic truss-, beam-, and plate-based lattice architectures, spinodoids are insensitive to manufacturing defects, scalable for high-throughput production, functionally graded by tunable local properties, and material failure resistant due to low-curvature morphology. However, the design of spinodoids is often hindered by the curse of dimensionality with an extremely large design space of spinodoid types, material density, orientation, continuity, and anisotropy. From a design optimization perspective, while genetic algorithms are often beyond the reach of computing capacity, gradient-based topology optimization is challenged by the intricate mathematical derivation of gradient fields with respect to various spinodoid parameters. To address such challenges, we propose a data-driven multiscale topology optimization framework. Our framework reformulates the design variables of spinodoid materials as the parameters of neural networks, enabling automated computation of topological gradients. Additionally, it incorporates a Gaussian Process surrogate for spinodoid constitutive models, eliminating the need for repeated computational homogenization and enhancing the scalability of multiscale topology optimization. Compared to ‘black-box’ deep learning approaches, the proposed framework provides clear physical insights into material distribution. It explicitly reveals why anisotropic spinodoids with tailored orientations are favored in certain regions, while isotropic spinodoids are more suitable elsewhere. This interpretability helps to bridge the gap between data-driven design with mechanistic understanding. To this end, we test our design framework on several numerical experiments. We find our multiscale spinodoid designs with controllable anisotropy achieve better performance than single-scale isotropic counterparts, with clear physics interpretations.