In this paper, we report a facile, rapid, and green strategy for the synthesis of cellulose/hydroxyapatite (HA) nanocomposites using an inorganic phosphorus source (sodium dihydrogen phosphate dihydrate (NaH₂PO₄·2H₂O)), or organic phosphorus sources (adenosine 5'-triphosphate disodium salt (ATP), creatine phosphate disodium salt tetrahydrate (CP), or D-fructose 1,6-bisphosphate trisodium salt octahydrate (FBP)) through the microwave-assisted hydrothermal method. The effects of the phosphorus sources, heating time, and heating temperature on the phase, size, and morphology of the products were systematically investigated. The experimental results revealed that the phosphate sources played a critical role on the phase, size, and morphology of the minerals in the nanocomposites. For example, the pure HA was obtained by using NaH₂PO₄·2H₂O as phosphorus source, while all the ATP, CP, and FBP led to the byproduct, calcite. The HA nanostructures with various morphologies (including nanorods, pseudo-cubic, pseudo-spherical, and nano-spherical particles) were obtained by varying the phosphorus sources or adjusting the reaction parameters. In addition, this strategy is surfactant-free, avoiding the post-treatment procedure and cost for the surfactant removal from the product. We believe that this work can be a guidance for the green synthesis of cellulose/HA nanocomposites in the future.