Abstract It is generally considered that photoacoustic imaging (PAI) and fluorescence imaging (FLI) cannot be enhanced concurrently, as they are dependent on competitive photophysical processes at the single‐molecule level. Herein, we reveal that BDTR9‐OC8 and BDTR9‐C8 , which have identical π‐conjugated backbones but are substituted by side chains of different rigidity, show distinct phototheranostic properties in the aggregated state. The NIR‐II FLI and PAI brightness of BDTR9‐C8 nanoparticles are enhanced by 4.6 and 1.4 times compared with BDTR9‐OC8 nanoparticles. Theoretical calculations and GIWAXS analysis revealed that BDTR9‐C8 with rigid side chains shows a relative amorphous condensed state, which will benefit the efficient transportation of photo‐generated excitons and phonons, subsequently enhancing the FLI and PAI signals. Besides, both nanoparticles exhibit excellent photothermal conversion efficiency due to their strong light‐harvesting capability and are considered effective photothermal therapy materials. This work provides an illuminating strategy for material design in the future.