Biocompatible hydroxyapatite (HAp) powders have thermodynamically driven tendencies to lower their surface areas due to the formation of irreversible aggregates. To address this challenge, HAp hybrid powders are herein prepared by using a traditional wet-precipitation method with subsequent hydrothermal carbonization for surface modification. The crystallite size, crystallite degree and area ratio of the infrared peak assigned to bonding water against those of free water are determined to investigate the variation of HAp crystallization with processing parameters. The crystallization of HAp is facilitated by enriched water in a stealth layer with water molecules evolved by citrate, nitrogen (N)-containing methylene blue (MB), hydrogen-group-rich β-cyclodextrin (CD) and oxygen-containing organic carbon shells. The low surface areas result in fabrication of nano-sized HAp powders with a uniform size distribution, well-dispersed morphologies and smooth surfaces through calcination of HAp-CD-MB@C. The pH values of acidic buffers increase slowly during incubation of HAp-CD-MB@C powders with chemical stability and a large grain size after calcination at 550°C for 2 h. The present study will shed light on the preparation of nano-sized inorganic powders with a uniform size distribution, well-dispersed morphologies and modulated chemical stability for potential applications as carriers of small molecular substances and fillers in composite materials.