Bone supports animal bodies, is the place where blood is produced, and is essential for the immune system, among other important functions. The dominant inorganic component in bone is hydroxyapatite (Hap), the structure and dynamics of which still pose many unsolved puzzles. An updated understanding of HAp is of great significance to osteology, dentistry, and the development of artificial bone and other biomaterials. In this work, HAp nanoparticles were synthesized with the wet chemical precipitation method and their structure and morphologies were controlled by varying pH and adding fluoride ions by two different routes: (1) fluoride ions were added during synthesis, and (2) fluoride ions were introduced after the samples were synthesized by soaking the samples in solutions with fluoride ions. XRD and HRTEM were employed to confirm the composition and structure, while various multinuclear (1H, 19F, 31P) solid-state nuclear magnetic resonance (NMR) methods including 1D single pulse, cross-polarization under magic-angle spinning (CPMAS), and 2D heteronuclear correlation (HETCOR) were used to characterize the structure, morphology, and dynamics, validating the general core-shell morphology in these F-HAp samples. It was found that all hydroxide ions were substituted when the fluoride ion concentration was above 0.005 M. An NMR peak corresponding to water structure emerged and the bulk water peak was shifted upfield, indicating that fluoride substitution modifies both the crystalline core and the amorphous shell of F-HAp nanoparticles. With the second route of fluoride substitution, increases in soaking time or fluoride ion concentration could increase fluoride substitution in HAp, but could not achieve complete substitution. Finally, with 1H-31P CPMAS and HETCOR, it was established that there are two types of phosphorous, one in the crystalline core (PO43−) and the other in the amorphous shell (HPO42−). These results are valuable for clarifying the fluoride substitution mechanism in HAp in biomaterials or in organisms, and provide insights for developing next generation replacement materials for bone, tooth, or coating films, drug delivery systems, etc.