The ordered assembly of molecules within a specific space of nanoscale, such as a surface, holds great promise in advanced micro-/nanostructure fabrication for various applications. Herein, we demonstrate the evanescent wave (EW)-guided organization of small molecules into a long-range ordered nanowire (NW) array. Experiment and simulation revealed that the orientation and periodicity of the NW array were feasibly regulated by altering the propagation direction and the wavelength of EW. The generality of this approach was demonstrated by using different molecule precursors. While existing studies on EW often took advantages of its near-field property for optical sensing, this work demonstrated the photochemical power of EW in the guided-assembly of small molecules for the first time. It also provides an enlightening avenue to periodic structure with fluorescence, promising for super-resolution microscopy and important devices applicable to optical and bio-related fields.