The solid-state ¹H, ³¹P NMR spectra and cross-polarization (CP MAS) kinetics in the series of samples containing amorphous phosphate phase (AMP), composite of AMP + nano-structured calcium hydroxyapatite (nano-CaHA) and high-crystalline nano-CaHA were studied under moderate spinning rates (5–30 kHz). The combined analysis of the solid-state ¹H and ³¹P NMR spectra provides the possibility to determine the hydration numbers of the components and the phase composition index. A broad set of spin dynamics models (isotropic/anisotropic, relaxing/non-relaxing, secular/semi-non-secular) was applied and fitted to the experimental CP MAS data. The anisotropic model with the angular averaging of dipolar coupling was applied for AMP and nano-CaHA for the first time. It was deduced that the spin diffusion in AMP is close to isotropic, whereas it is highly anisotropic in nano-CaHA being close to the Ising-type. This can be caused by the different number of internuclear interactions that must be explicitly considered in the spin system for AMP (I–S spin pair) and nano-CaHA (I_N–S spin system with N ≥ 2). The P–H distance in nano-CaHA was found to be significantly shorter than its crystallographic value. An underestimation can be caused by several factors, among those – proton conductivity via a large-amplitude motion of protons (O–H tumbling and the short-range diffusion) that occurs along OH⁻ chains. The P–H distance deduced for AMP, i.e. the compound with HPO₄²⁻ as the dominant structure, is fairly well matched to the crystallographic data. This means that the CP MAS kinetics is a capable technique to obtain complementary information on the proton localization in H-bonds and the proton transfer in the cases where traditional structure determination methods fail.