<p>A geometric close-packing framework for nuclear structure is introduced, delivering parameter-free predictions for neutron–proton (<i>np</i>) short-range correlation (SRC) pair counts across the nuclear chart. Motivated by QCD-inspired parton flux tubes and electromagnetic resonance phenomena observed in BESIII measurements, each nucleon is represented by a closed double-helix parton flux tube configuration following a toroidal trefoil-knot trajectory and assembling into concentric toroidal shells sharing a common centroid. Within this framework, SRCs arise naturally as nearest-neighbor contacts between adjacent flux tube segments, converting SRC counting into a deterministic consequence of spatial organization rather than a phenomenological input. The resulting <i>np</i>-SRC counts quantitatively reproduce CLAS measurements for C, Al, Fe, and Pb and are consistent with established experimental systematics. The geometry further indicates a set of correlated features of <i>np</i>-SRC dynamics: (i) each nucleon participates in at least one <i>np</i>-SRC pair; (ii) adding neutrons increases the fraction of high-momentum protons; and (iii) adding protons increases the fraction of high-momentum neutrons. These results suggest that short-range nuclear dynamics is governed by an underlying geometric organizing principle, offering a physically transparent mechanism for the emergence of SRCs in nuclei.</p>