AbstractUnlocking the 3‐D structure and properties of intact chondritic porous interplanetary dust particles (IDPs) in nanoscale detail is challenging, which is also complicated by atmospheric entry heating, but is important for advancing our understanding of the formation and origins of IDPs and planetary bodies as well as dust and ice agglomeration in the outer protoplanetary disk. Here, we show that indigenous pores, pristine grains, and thermal alteration products throughout intact particles can be noninvasively visualized and distinguished morphologically and microstructurally in 3‐D detail down to ~10 nm by exploiting phase contrast X‐ray nanotomography. We have uncovered the surprisingly intricate, submicron, and nanoscale pore structures of a ~10‐μm‐long porous IDP, consisting of two types of voids that are interconnected in 3‐D space. One is morphologically primitive and mostly submicron‐sized intergranular voids that are ubiquitous; the other is morphologically advanced and well‐defined intragranular nanoholes that run through the approximate centers of ~0.3 μm or lower submicron hollow grains. The distinct hollow grains exhibit complex 3‐D morphologies but in 2‐D projections resemble typical organic hollow globules observed by transmission electron microscopy. The particle, with its outer region characterized by rough vesicular structures due to thermal alteration, has turned out to be an inherently fragile and intricately submicron‐ and nanoporous aggregate of the sub‐μm grains or grain clumps that are delicately bound together frequently with little grain‐to‐grain contact in 3‐D space.