Three perylene tetracarboxylic diimide (PDI) trimers substituted with different side groups at the bay positions were prepared with the triazine ring as a linkage. The free rotation of C-N-C bonds between the triazine ring and the PDI unit provide these molecules with some flexibility. The UV-vis absorption and fluorescence spectra of these three compounds show different concentration-dependent behaviors, which depend on the side groups at the bay positions. Significant aggregation in organic solvents was revealed by the electronic absorption and emission spectra as well as the fluorescence quantum yield calculation. The aggregation behavior of these compounds in the solid state were investigated by X-ray diffraction (XRD), and the morphology of the aggregates was examined by atomic force microscopy (AFM). The aggregation of trimer 1 with two phenoxy groups at the 1 and 7 positions results in long nanofibers whereas trimers 2 and 3 with dipiperidinyl groups or tetraphenoxyl groups at the bay positions form only particles. The results of this research revealed that PDI trimers with flexible structures can also self-assemble into large ordered aggregates such as those with rigid structure. This information is believed to be useful in the design of novel nanoorganic materials.