Further advancement in the research area of covalent organic frameworks (COFs) is in urgent need of structural information with high accuracy. The bottleneck in characterization is the lack of effective strategies to resolve the complex features (e.g., the stacking sequence) of hierarchical structures. Herein, we establish an NMR crystallographic protocol to systematically and precisely measure multinuclear distances through advanced dipolar recoupling techniques, such as rotational echo double resonance (REDOR), double quantum-single quantum (DQ-SQ), and rotational echo adiabatic passage double resonance (REAPDOR) experiments. For the first time, we obtained the atomic distances of 1H-1H, 1H-19F, and 13C-19F within the monolayer, two adjacent layers, and three consecutive layers of a two-dimensional (2D) COF, TPPA-F4. Based on these key parameters with an accuracy of 0.10 Å, the structural features of TPPA-F4 COF, including the covalent connection, intralayer conformation, interlayer distance, the direction and distances of the layer offsets, and stacking mode, have been de novo determined in detail. Moreover, the generality of this NMR crystallographic approach was verified by solving the crystal structure of a selective deuterium-labeled TPPA-d4 COF via 1H-2H distance measurements. We expect that the NMR crystallographic protocol paves new ways not only for the structural determination of complex 3D COFs but also for the investigation of the crystallization process and dynamic behaviors of COFs with high spatiotemporal resolution. In addition, the selective deuteration strategy developed herein enabled the first NMR measurement of 1H-2H distances in materials research, which may find broad applications for the characterization of weak interactions in solids.