In this work, perylene bisimide derivatives (PBI-1 and PBI-2) with tertiary amine groups were designed and synthesized. To control the final morphologies and properties of their aggregates, seven kinds of organic acids were used to alter the self-assembly environment. The influence of organic acids on the morphology of the aggregates was investigated. Photophysical properties of the aggregates were markedly affected by the kind and concentration of the organic acid. The thermal and gas sensitivities of the PBI-1 aggregates were studied with the use of UV–visible spectroscopy and digital imaging. The shift of the UV–visible spectra varied with time, temperature, acid type and acid concentration. Furthermore, PBI-1 aggregates showed a red-to-blue color change after addition of seven organic acids, whereas the color of the PBI-2 aggregates remained red. These changes of morphologies, photophysical properties and their thermal and gas sensitivities make these aggregates potentially useful in the fields of optoelectronics or sensors.