The stacking mode in aggregate state results from a delicate balance of supramolecular interactions, which closely affects the optoelectronic properties of organic π-conjugated systems. Then, managing these interactions is crucial for advancing phototheranostics, yet remains challenging. A subtle strategy involving peripheral phenyl groups is debuted herein to transform X-aggregated SQ-H into J-aggregated SQ-Ph, reorienting intermolecular dipole interactions while rationally modulating π-π interactions. Co-assembled with liposomes (DSPE-PEG2000), SQ-Ph nanoparticles (NPs) exhibit low toxicity, superior biocompatibility, and a bathochromic shift to the 1064 nm match-excited NIR-II region, with a fluorescence brightness (ε