Modulating the assembly pathway is an indispensable strategy for optimizing the performance of optical materials. However, implementing this strategy is nontrivial for metal nanocluster building blocks, due to the limited functional modification of nanoclusters and complexity of their emission mechanism. In this report, we demonstrate that a gold nanocluster modified by 4,6‐diamino‐2‐pyrimidinethiol (DPT‐AuNCs) self‐assembles into two distinct aggregation structures in methanol (MeOH)/water mixed solvent, thus exhibiting pathway complexity. Kinetic studies show that DPT‐AuNCs firstly assembles into non‐luminescent nanofibers (kinetically controlled), which further transforms into strongly luminescent microflowers (thermodynamicallycontrolled). In‐depth analysis of the assembly mechanism reveals that the transformation of aggregation structures involves the disassembly of nanofibers and a subsequent nucleation‐growth process. Temperature‐dependent photoluminescence (PL) spectroscopy and infrared (IR) measurements reveal that inter‐cluster hydrogen bonding bridged by solvent molecules and C‐H···π interaction are the key factors for emission enhancement. The photoluminescent property of DPT‐AuNCs can be controlled by varying the cosolvent in water, enabling DPT‐AuNCs to distinguish different kind of alcohols, particularly the isomerism n‐propanol (NPA) and isopropanol (IPA). Additionally, he addition of seeds effectively regulate the assembly kinetics of DPT‐AuNCs. This study advances our understanding of assembly pathways and improves the luminescent performance of nanoclusters (NCs).