Natural polysaccharides play an important role in the formation of nanohydroxyapatite (nHA) crystals in biological systems. In this study, we synthesized nHA crystals in the presence of four polysaccharides, i.e., pectin, carrageenan, chitosan, and amylose, referred as PeHA, CaHA, CsHA, and AmHA, respectively. X-ray diffraction, Fourier transform infrared spectroscopy, transmission electron microscopy, scanning electron microscope, and thermogravimetric analysis were used to investigate the formation of nHA crystals. The shape of prepared nHA crystals is needle/rod-like in all cases, whereas the size increases in the order of PeHA, CaHA, CsHA, and AmHA. The presence of polysaccharides induces the heterogeneous nucleation of nHA and further modulates the crystal growth. Our data suggest that the interaction intensity between nHA and polysaccharides is in the decreasing order of PeHA, CaHA, CsHA, and AmHA, resulting in the smallest nHA crystals with pectin. It is also demonstrated that a high polysaccharide concentration and short reaction time are adverse to nHA crystals, especially for the polysaccharides with carboxyl groups. This study can provide insight into the effects of polysaccharides with different chemical functional groups (−COOH, −OSO3H, −NH2, −OH) on the formation of nHA crystals.