Nuclear magnetic resonance (NMR) is a powerful method for determining the structure of molecules and proteins [1]. While conventional NMR requires averaging over large ensembles, recent progress with single-spin quantum sensors [2][3][4][5][6][7][8][9] has created the prospect of magnetic imaging of individual molecules [10][11][12][13]. As an initial step towards this goal, isolated nuclear spins and spin pairs have been mapped [14][15][16][17][18][19][20][21]. However, large clusters of interacting spins -such as found in molecules -result in highly complex spectra. Imaging these complex systems is an outstanding challenge due to the required high spectral resolution and efficient spatial reconstruction with sub-angstrom precision. Here we develop such atomic-scale imaging using a single nitrogen-vacancy (NV) centre as a quantum sensor, and demonstrate it on a model system of 27 coupled 13 C nuclear spins in a diamond. We present a new multidimensional spectroscopy method that isolates individual nuclearnuclear spin interactions with high spectral resolution (< 80 mHz) and high accuracy (2 mHz). We show that these interactions encode the composition and inter-connectivity of the cluster, and develop methods to extract the 3D structure of the cluster with sub-angstrom resolution. Our results demonstrate a key capability towards magnetic imaging of individual molecules and other complex spin systems [9][10][11][12][13].The nitrogen-vacancy (NV) centre in diamond has emerged as a powerful quantum sensor [2-13, 22, 23]. The NV electron spin provides long coherence times [5, 6,20] and high-contrast optical readout [5,24,25], enabling high sensitivity over a large range of temperatures [5, 6,20,25,26]. Pioneering experiments with near-surface NV centers have demonstrated spectroscopy of small ensembles of nuclear spins in nano-scale volumes [2, 3,[5][6][7][8], and electron-spin labelled proteins [4]. Furthermore, single nuclear spin sensitivity has been demonstrated and isolated individual nuclear spins and spin pairs have been mapped [14][15][16][17][18][19][20][21]. Together, these results have established the NV center as a promising platform * T.H.Taminiau@TUDelft.nl for magnetic imaging of complex spin systems and single molecules [10][11][12][13].In this work, we realise a key ability towards that goal: the 3D imaging of large nuclear-spin structures with atomic resolution. The main idea of our method is to obtain structural information by accessing the couplings between individual nuclear spins. The key open challenges are: (1) to realize high spectral resolution so that small couplings can be accessed, (2) to isolate such couplings from complex spectra, and (3) to transform the revealed connectivity into the 3D spatial structure with sub-angstrom precision.The basic elements of our experiment are illustrated in Fig. 1a. We consider a cluster of 13 C nuclear spins in the vicinity of a single NV centre in diamond at 4 K. This cluster provides a model system for the magnetic imaging of single molecules and spin ...