A flow-micro-reactor system was employed to fabricate hydroxyapatite (HAp) in order to mimic the interface between calcium and phosphate solutions on a wet chemical procedure. The mixing ratio of calcium nitrate tetrahydrate and diammonium hydrogenphosphate solution was set to the stoichiometric atomic ratio HAp, 1.67, while pH value of the product suspension was varied from 6.4 to 10.0. The product morphology was changed from nano-sheet type to nano-particle type via nano-rod one, while their size was decreased from 100–500 nm to 50 nm. All as-prepared samples, irrespective of pH value of the resultant suspension, consisted of HAp, predominant phase, octacalcium phosphate (OCP), and dicalcium phosphate dihydrate (DCPD) or dicalcium phosphate anhydrate (DCPA). A batch system using the same solutions yielded very similar results, which confirmed that the reactions in this micro-reactor well reproduced a large-scale mixing system. Calcining sample obtained from pH 6.4 suspension for 2 h at lower temperatures (<400°C) lead to decomposition of DCPD, DCPA, and OCP. Trace tricalcium phosphate (TCP) appeared on calcination above 400°C. HAp remained the predominant phase throughout the process. After calcination at 600°C, no other phases than HAp and TCP were present in the product. The analyzed ratio Ca/P (1.38) implied that those crystalline phases were highly Ca-deficient, and that amorphous calcium phosphates were involved in both as-prepared and calcined sample pH 6.4.