Low mobility and solubility reduce the availability of traditional phosphorus (P) fertilizer in red acidic soil. Hydroxyapatite (HAP), especially nano-hydroxyapatite (n-HAP), may be more efficient than P fertilizer because of its nanoparticle characteristics. Camellia oleifera (C. oleifera) is an edible oil tree whose productivity is greatly affected by P fertilizer. During this study, we investigated the migration of different particle sizes of HAP (20 nm, 200 nm, and 80 μm) and their effects on the seedling growth of C. oleifera cultivar Huashuo (HS) cuttings. A column experiment showed that the efflux ratio was negatively correlated with particle size in red acidic soil. The leaching results revealed that the contents of total P and available P in the 20-nm treatment were significantly higher than those in the 200-nm and 80-μm treatments in the deep soil (10–15 cm or 15–20 cm), whereas the application of 20-nm n-HAP caused 13.43% wastage of available P. During the container experiments, 200-nm and 20-nm HAP significantly promoted the growth of the seedlings in terms of seedling height, stem diameter, and biomass. The available P contents in the rhizosphere and nonrhizosphere soils were negatively correlated with the HAP particle sizes. In conclusion, the migration of HAP is inversely correlated with particle size, and HAP improves the P bioavailability in red acidic soil. In summary, 200-nm HAP was the best P fertilizer for the seedlings of HS among the three particle sizes. This study offers preliminary results indicating that 200-nm HAP might be a better P fertilizer compared with other two HAP particle sizes for use in future C. oleifera orchards.