Cluster substitution can effectively regulate the physicochemical properties of two-dimensional (2D) materials and has been applied in fields such as catalysis and magnetism. However, the intrinsic mechanism of its regulation of thermal transport properties and the impact of clusters on optical and mechanical properties are not yet clear. In this work, 2D T-Cu6S2 is obtained by replacing the transition metal element M of 2D T-MS2 with the Cu6 clusters. Then, based on the first-principles method, we systematically studied the thermal transport, mechanical, and optical properties of T-Cu6S2. The results show that introducing Cu6 clusters reduces the phonon vibration frequency, and enhances phonon scattering, that is, the coupling effect of harmonic weakening and anharmonic enhancement. This makes the lattice thermal conductivity of T-Cu6S2 at the four-photon level reduced to 0.18 W/mK (at 300 K), which is much lower than that of traditional 2D T-MS2. In addition, we found that the introduction of clusters changes the crystal and electronic structures of T-Cu6S2, enhances the flexibility and ductility of T-Cu6S2, and increases its transmission ability for visible light and ultraviolet light. This study provides insights into the regulation of multiple properties of 2D materials, which benefits the development of 2D functional materials.