The aggregation of dyes is of considerable importance in relating to their functions and applications. In this paper, we have investigated the regulation on the aggregation and morphology of two cyanine dyes, 3,3'-disulfopropyl-4,5,4',5'-dibenzo-9-methylthiacarbocyanine triethylammonium salt (MTC) and 3,3'-disulfopropyl-4,5,4',5'-dibenzo-9-phenylthiacarbocyanine triethylammonium salt (PTC), using a series of gemini amphiphiles (bis(2'-heptadecyl-3'-ethylimidazolium)-1,n-alkane dibromide, abbreviated as Gn, n = 2, 4, 6, 8, 10). It has been found that both of the dyes could be adsorbed onto the monolayers of the gemini amphiphiles through the electrostatic and pi-pi interaction and stacked into H- or J-aggregate. The spacer of the gemini amphiphile showed good control over the aggregation of MTC: H-aggregate was favored when gemini amphiphiles with short spacer were applied, while J-aggregation was preferred in the case of longer spacer. Only J-aggregate was observed for PTC on gemini monolayer, regardless of the structure of the gemini amphiphiles. Interesting morphologies were observed for all the gemini/dye complex monolayers. Network structure and nanofibers were formed for the gemini/MTC films transferred below the plateau surface pressure and close to the collapse pressure, respectively. The ability of the complex monolayers to form nanofibers strongly depended on the component amphiphiles, G2 > G4 > G6, and no nanofibers were observed for G8/MTC and G10/MTC after the collapse. Only squared domains were observed for gemini/PTC monolayers. When both G2 and G10 were mixed, an individual control of the gemini amphiphiles over the aggregation of MTC in the complex monolayers was observed. The relationship among the spacer, dye structure, and aggregation was revealed.