Organic π-conjugated semiconductors (OCSs) have recently emerged as a promising alternative to traditional inorganic materials for photocatalysis. However, the aggregation of OCSs in photocatalytic aqueous solution caused by self-assembly, which closely relates to the photocatalytic activity, has not yet been studied. Here, the relationship between the aggregation of 4,7-Bis(thiophen-2-yl) benzothiadiazole (TBT) and the photocatalytic activity was systematically investigated by introducing and varying the position of methyl side chains on the two peripheral thiophene units. Experimental and theoretical results indicated that the introduction of -CH3 group at the 3-position of TBT resulted in the smallest size and best crystallinity of aggregates compared to that of TBT, 4- and 5-positions. As a result, TBT-3 exhibited an excellent photocatalytic activity towards H2 evolution, ascribed to the shorten charge carrier transport distance and solid long-range order. These results suggest the important role of aggregation behavior of OCSs for efficient photocatalysis.