The effective diffusivity of ionic species in multiphase materials is critical for the design and function of composite materials for electrochemical energy storage. In practice, effective diffusivity depends sensitively not only on the intrinsic diffusivities of constituting materials but also on their topological arrangement; nevertheless, these coupled contributions are oversimplified in most analytical models. Here, we combine atomistically informed mesoscale modeling and machine learning (ML) analysis to unravel how such features affect effective diffusivity in two-phase composites. Using the Li7La3Zr2O12-LiCoO2 composite solid-state battery cathode as a model system, we compute effective diffusivity for 600 distinct dense polycrystalline microstructures with different topological configurations of grains, grain boundaries, and heterointerfaces. We verify that in addition to atomic-scale variabilities, microstructural feature diversity can significantly impact effective transport properties. Across the ensemble of test microstructures, this often results in bimodal distributions of effective diffusivity that encompass two qualitatively distinct operating mechanisms, which we identify via flux analysis. An ML approach reveals that the most critical determining factors for effective diffusivity are the connectivity of bulk phases and their heterointerfaces. The role of ionic mobility at the heterointerfaces is also discussed. These insights highlight the combined importance of microstructure and interface engineering in tuning the transport properties of ionic species in composite materials. Our framework can also be extended for understanding generic microstructure-property relationships in other complex multiphase materials.