For nanocrystals (NCs) self-assembly, understanding the chemical and supramolecular interactions among building blocks is significant for both fundamental scientific interests and rational nanosuperstructure construction. However, it has remained an extreme challenge for many self-assembly systems due to the lack of appropriately quantitative approaches for the corresponding exploration. Herein, by combination of the proposed colorimetric method for cationic surfactant quantitation and all-atom simulations, we manage to present a clear chemical picture for the thiol molecules modulated self-assembly of gold nanorods (GNRs), one of the earliest and most convenient methods for the fabrication of freestanding GNR self-assemblies. It is revealed that the self-assembly of GNRs is driven by the hydrophobic effects of the alkyl chains of the modified cationic surfactants, as their bilayer structure is destroyed by the added thiol molecules. In other words, the actual roles of the thiol molecules for causing GNRs assembly are indirectly inductive effects instead of the previously believed direct electrostatic attraction and/or hydrogen-bond linking effects of the binding thiol molecules. Furthermore, the GNRs exhibit diameter-dependent assembly behaviors: thicker GNRs tend to adopt the end-to-end assembly mode, while thin ones prefer the side-by-side assembly mode, further demonstrating that hydrophobic effects among the build blocks are the driving force for the GNRs assembly.