Supramolecular self-assembly of near-infrared (NIR) dyes are believed to be a promising strategy to design effective photothermal agents for tumor photothermal therapy (PTT). However, due to the uncontrollable intermolecular interactions, accurately fine-tuning the aggregated morphology of NIR dyes through adjusting their supramolecular self-assembly is challenging. Here, based on organic-metal coordination interaction, a facile self-assembly fine-tuning strategy is proposed to adjust the aggregated morphology of heptamethine cyanine (Cy7) dyes, the well-known NIR dyes. Three hydrophilic Cy7 derivatives Cy-nCOOH (n = 1, 2, and 3) are synthesized, and then are coordinated with Cu 2+ to obtain different aggregates. Cy-1COOH/Cu aggregates form partial J-aggregates. Cy-2COOH/Cu aggregates are amorphous. Noteworthily, Cy-3COOH/Cu aggregates exhibit significant H-type aggregation. Moreover, Cy-3COOH/Cu aggregates show about threefold higher photothermal conversion efficiency and obviously enhanced photostability than Cy-1COOH/Cu and Cy-2COOH/Cu aggregates. It is demonstrated that H-aggregates with face-to-face π-π stacking greatly quench fluorescence and inhibit singlet oxygen ( 1 O 2 ) production, which lead to the improved photothermal performances. In vitro and in vivo experiments demonstrate the remarkable tumor PTT efficiency of Cy-3COOH/Cu H-aggregates. This study provides a new insight into how to precisely control molecular aggregation of organic dyes in supramolecular self-assembly for enhanced tumor phototherapy.