Shark enameloid has excellent mechanical properties that are comparable to human enamel. Yet, interestingly, the growth rate of shark tooth is very fast, which could provide inspiration for materials fabrication techniques. However, the factors that could facilitate the fast biomineralization of enameloid are unclear. Here, we studied the crystallization mechanism and growth kinetics of enameloid-like densely aligned fluorapatite (FAP) nanorod arrays on the surface of shark tooth transverse slices. To investigate the effects of the ion transportation rate and fluoride concentration, experiments were carried out by controlling the addition of the phosphate solution into the calcium solution, instead of merely immersing the tooth slice in premixed solution of calcium and phosphate. We demonstrated that amorphous nanoparticles of less than 10 nm in diameter were first generated in mineralization solution, and the growth of FAP crystallites proceeded by the attachment of nanoparticles, preferentially along the c axis of the crystallites. Subsequently, the coalescence and fusion of adjacent crystallites lead to the formation of larger nanorods. We also found that both the appropriate flow rate of phosphate solution, such as 0.212 μl s−1, and a high fluoride concentration could accelerate the growth of the FAP layer. This work implied that the rapid growth of enameloid might be facilitated by the special ionic microenvironment of the enameloid matrix. Overall, these results further improve our understanding of the biomineralization process and provide a theoretical foundation for efficient synthesis of biomimetic materials.