Topological insulators (TIs) have attracted tremendous interest in the context of thermoelectrics (TE) as they are often composed of materials used for making effective and practical TE devices, while their exotic surface state electronic structures can be a promising candidate for decoupling thermal and electrical transport. However, common strategies used to improve TE performance such as using superlattices, heterostructures or alloying can often obscure the prominence of the unique properties of the topological surface states in TIs. Furthermore, obtaining a large enhancement in the TE performance in extremely thin films of these materials, required for cooling of these thin films, along with precise experimental demonstrations of the coexisting and distinct contributions of the bulk and surface states to the TE transport, still remains a challenging task. In this work, we engineer low-dimensional nanostructures onto thin TI films to drastically improve their TE performance while retaining their unique topological surface state properties. We demonstrate a large suppression of thermal conductivity, by nearly an order of magnitude, in a thin nanostructured Bi2Te2Se film without significantly affecting its electrical conductivity. The measured thermal conductivity of nanostructured TI films is lower than other reported values for thin film TIs and approaches the amorphous limit, indicating highly disordered thermal transport. This results in an enhancement in the figure-of-merit zT by a factor ∼11 times than that of pristine thin Bi2Te2Se films at room temperature. The zT can be further enhanced using optical helicity-dependent control over the transport of the surface state electrons due to their unique spin-orbit coupling. The obtained zT is higher than values reported in other thin film TIs, positioning our Bi2Te2Se system as a promising alternative to more complex structures and materials. Additionally, we investigate the importance of the relative contribution of the surface states and the bulk to TE transport which points out the directions of further improvement of TE properties. Overall, this study provides critical experimental insights for developing high-performance TE materials utilizing the unique properties of thin film TIs combined with the benefits of nanostructuring.