We propose a novel approach to probe primordial inhomogeneity in hot and dense matter which could be realized in noncentral heavy-ion collisions. Although the Hanbury Brown and Twiss (HBT) interferometry is commonly used to infer the system size, the cluster size should be detected if substructures emerge in space. We demonstrate that a signal peak in the HBT two-particle correlation stands at the relative momentum corresponding to the spatial scale of pseudo one-dimensional modulation. We assess detectability using the data prepared by an event generator (AMPT model) with clustering implemented in the particle distribution.