The good bioactivity of hydroxyapatite (HA) makes it become a popular biomaterial, and so, the synthesis of HA has attracted much attention. However, a simple method to prepare well-dispersive and ultrafine HA nanoparticles (NPs) still needs to be explored. Here, needle-like hybrid HA NPs were synthesized in the presence of alginate (ALG) and the mechanism of ALG regulation on forming HA/ALG hybrid NPs was investigated. The size and crystallinity of HA/ALG NPs could be controlled simply by varying the amount of ALG. With a higher concentration of ALG, the size of HA/ALG NPs reduced and their dispersity was further improved. The assembly with ca. 3-6 nm thick nanoneedles was discernible in HA/ALG NPs. The results collected by Ca2+ concentration, pH, and conductometric measurements further provided the supportive data for ALG inhibition of calcium phosphate compound formation and thus modulation of HA crystallization. In addition, the good biocompatibility of synthesized HA/ALG NPs was indicated from the results of CCK-8 assays and CLSM observations after cultured with L929 cells. The needle-like HA NPs are promising for varied biomedical purposes, and their potential application as drug carriers would be further studied.