Inner transition metal ions doped layered double hydroxides–embedded in CNTs have attracted increasing attention for wastewater treatment and renewable energy recently. In this work, the nanostructures of Al-Li/Th-LDH@CNT consisting of flower-like morphology were successfully synthesized by the elegant combination of exfoliated Al-Li/Th LDHs nano-sheets and F-CNTs using the hydrothermal method. The as-synthesized Al-Li@ThLDH-CNT nanocomposite is employed for MG dye photodegradation and selective adsorption of Cr (VI) ions. The Al-Li/Th-LDH@CNT nanocomposite has exhibited excellent visible-light-induced photocatalytic activity towards Malachite green (MG) dye, and almost 98% of (MG) dye is decolorized within 45 min. Studies probing the mechanism demonstrate that the photogenerated hydroxyl radical and holes play a vital role in the MG dye degradation process. Furthermore, the Al-Li/Th-LDH@CNT was tested to examine its selective adsorption behavior towards different metal ions at ultra-low trace levels by the ICP-MS technique. The adsorption behavior of Al-Li/Th-LDH@CNT displayed high removal percentage towards Cr6+ (94.1%), while as 86.7% and 83% for Al-Li and Al-Li-CNT adsorbents and the maximum adsorption capacities of Al-Li, Al-Li-CNT, and Al-Li/Th-LDH@CNT were found to be 156.2, 163.3 and 172.4 mg/g respectively. Thus, preparing layered structure composite using a simple engineered route may open a new strategy to synthesize advanced materials having improved synergistic catalytic properties, which could be effectively used as highly efficient probes for environmental applications.