The human genome comprises roughly two meters of DNA folded into a nucleus only ten micrometers across, yet how this compaction is achieved — and how it shapes gene regulation — remains poorly understood. The problem extends beyond DNA: RNA is roughly five times more abundant than DNA in the cell, and its spatial positioning relative to genome structure is largely uncharacterized. Existing approaches capture either contact frequency or spatial position, but rarely both in the same cell, and none resolve DNA folding and RNA localization together at single-cell resolution. Here we combine whole-genome fluorescence in situ hybridization (FISH) with single-cell Hi-C (scHi-C) performed on the same individual cells to reconstruct high-resolution three-dimensional genome structures. FISH imaging of 900 probes at 3 Mb resolution provides a spatial scaffold that anchors the reconstruction in absolute coordinates, while scHi-C contacts fill in the intervening structure, yielding models with detail beyond what either measurement achieves alone. To place RNA within these structures, we extend the proximity ligation chemistry to capture RNA-containing contacts alongside genomic ones, so that RNA molecules are recorded together with their chromatin interaction partners in the same experiment and can be positioned directly within the reconstructed structure. Together, these measurements yield single-cell 3D genome structures with RNA positions resolved in situ, providing a direct view of how genome folding and RNA distribution are coupled and how that coupling varies between individual cells.