Aggregation plays a critical role in modulating the photophysical process of organic molecules. However, the rational control of the construction of a function-oriented stacking mode for efficient photothermal (PT) conversion in the second near-infrared region (NIR-II; 1000–1700 nm) remains a challenge. Herein, an H-aggregation of 3,3′,5,5′-Tetramethylbenzidine (TMB)–TMB dication (TMB++) complexes in linear agarose (H-TTC/LAG) with narrowed band gap (0.96 eV) was fabricated through intermolecular hydrogen-bonding interactions between the amino groups of TTC and the peripheral hydroxyl groups of LAG. Charge-transfer mechanism and H-aggregation ensured NIR-II absorption of the complex at >1400 nm. The H-aggregation also promoted a non-radiation relaxation pathway and improved the thermal stability of TTC, which together favored the constructed H-TTC/LAG with ultra-efficient PT conversion that increased rapidly to 140 °C in 15 s under the NIR-II laser (1064 nm, 1.0 W cm−2) irradiation. Such a unique H-TTC/LAG with good biocompatibility was used to demonstrate a superior PT therapy via high-efficiency tumor growth inhibition in mouse mammary carcinoma (4T1) the BALB/c mice tumor-bearing xenografts. This is the first established H-aggregation of charge-transfer complexes in a noncovalent system, which not only provides a new strategy to develop ultra-efficient NIR-II PT materials but also paves the way for constructing functional materials with aggregates of charge-transfer complexes.