High exposure to radioactive metal ions, such as uranium (U(VI)) and cesium (Cs(I)), potentially has adverse effects and can cause severe health problems leading to a number of specific diseases. This study primarily aims to facile synthesis self-functionalized mesoporous ion-exchanger for the removal of trace concentrations of radioactive ions from water in an efficient way. The fabricated mesoporous flaky flower-like hydroxyapatite ion-exchanger (MFF-HAp) with its 3D hexagonal mesopore structure has advantages of high surface area, natural surfaces, and active acid sites can strongly induce ion-exchange with uranyl and cesium ions. It was characterized by X-ray diffraction (XRD), fourier infrared spectroscopy (FTIR), scanning electron microscopy (SEM), high resolution transmission electron microscope (HR-TEM), energy dispersive X-ray (EDX) spectroscopy, N2 adsorption/desorption and thermal analysis (TGA/DTA). From the engineering point of view, it offers a simple and one-step capture procedure for the decontamination of Cs(I) and U(VI) from their solutions. The interesting findings in this study are the ion-selectivity exhibited by MFF-Hap toward the target U(VI) and Cs(I) ions in environmental and nuclear waste disposal samples, and its reproducibility/durability over a number of regeneration cycles. These unique properties of MFF-HAp ion-exchanger render it as promising durable material for efficient radioactive species accommodation.