Recently, there is a rise in demand for low-cost natural source-derived photocatalysts for the degradation of harmful dyes. Here, we report new mesoporous g-C3N4/HAp nanocomposites prepared by a simple hydrothermal method for efficient photocatalytic degradation of rhodamine B (RhB) dye. Ultrafine g-C3N4 nanosheets were synthesized from the polymerization of melamine and exfoliation of bulk g-C3N4. HAp nanoparticles were obtained by mixing mussel shell powder with Na2HPO4 and microwave irradiation of the mixture. The g-C3N4 (1–3 wt%)/HAp was produced from hydrothermally reacting g-C3N4 and HAp. XRD analysis of g-C3N4/HAp confirms the presence of g-C3N4 and HAp phases. From FT-IR, Raman, NMR, and XPS spectra, the chemical bonds of g-C3N4/HAp were confirmed. The microscopic (SEM, TEM, and AFM) images illustrate the fine fusion of g-C3N4 and HAp. BET and TG/DTA studies reveal that the g-C3N4/HAp is mesoporous in nature and is thermally stable. Optoelectronic properties indicate that g-C3N4/HAp’s luminescence changes with the g-C3N4 concentration. In addition, g-C3N4/HAp showed high photocatalytic efficiency for RhB degradation (99%) in comparison to g-C3N4 and HAp. The g-C3N4/HAp is recyclable and possesses good photochemical stability. Superoxide and hydroxyl radicals play a key role in the photodegradation of RhB. A reaction mechanism involving charge (electrons, holes) transfer at Z-scheme heterojunction of g-C3N4/HAp is proposed. This ‘green’ method, of g-C3N4/HAp synthesis from g-C3N4 and biowaste-derived HAp, can potentially be applied for catalytic removal of pollutants from industrial effluents.