Various morphologies of copper (II) oxide (CuO) such as dandelion, sea anemone, walnut, leaf, dendrite, rod, fiber, feather, and flake were synthesized and characterized by different methods. The oxidation of indole (IND) and benzothiophene (BT) in mild conditions was studied by various morphologies of CuO. Walnut with the lowest surface area 7.928 (m2g−1) and rod with a high surface area 41.237 (m2g−1) had efficiencies of 5.93% and 91.44% for IND and 0.53% and 88.29% for BT at 4 h, respectively. Zeolite MWW was synthesized by microwave and hydrothermal method on which CuO rod was loaded via wet impregnation method. The results indicated that CuO rod/MWW composite considerably outperformed CuO rod. The oxidations of IND and BT by CuO rod/MWW composite for 75 min was 99.99 and 97.67%, respectively. Based on the results across all experiments, the oxidation of the IND was higher than that of BT. CuO rod/MWW composite was shown to be an efficient catalyst for oxidation of nitrogen and sulfur heterocycles.