Stochastic heterogeneous microstructures are widely applied in structural and functional materials, playing a crucial role in determining their performance. X-ray tomography and focused ion beam serial sectioning are frequently used methods to reconstruct three-dimensional (3D) microstructures, yet are demanding techniques and are resolution-limited. Here, a high-throughput multi-stage 3D reconstruction method via distance correlation functions is developed using a single representatively large-sized 2D micrograph for stochastic microstructures, and verified by X-ray micro-tomography datasets of isotropic and anisotropic solid oxide fuel cell electrodes. This method provides an economic, easy-to-use and high-throughput approach for reconstructing stochastic heterogeneous microstructures for energy conversion and storage devices, and can readily be extended to other materials.