Organic photothermal materials based on conjugated structures have significant potential applications in areas such as biomedical diagnosis, therapy, and energy conversion. Improving their photothermal conversion efficiency through molecular design is critical to promote their practical applications. Especially in similar structures, understanding how the position of heteroatoms affects the conversion efficiency is highly desirable. Herein, we prepared two isomeric small D-A molecules with different sulfur atom positions (TBP-MPA and i-TBP-MPA), which display strong and broad absorption in the UV-visible region due to their strong intramolecular charge transfer characteristics. Compared to i-TBP-MPA, TBP-MPA demonstrates aggregation-induced photothermal enhancement (AIPE). Under simulated sunlight (1 kW m-2) irradiation, the stable temperature of TBP-MPA powder reached 60 °C, significantly higher than the 50 °C achieved by i-TBP-MPA. Experimental and theoretical results indicate that the S⋯N non-covalent interactions in TBP-MPA impart a more rigid conjugated framework to the molecule, inducing ordered molecular stacking during aggregation. This ordered stacking provides additional non-radiative transition channels between TBP-MPA molecules, enhancing their photothermal performance in the aggregated state. Under 1 sun irradiation, TBP-MPA achieved a water evaporation rate of 1.0 kg m-2 h-1, surpassing i-TBP-MPA's rate of 0.92 kg m-2 h-1.