Herein, we report design, synthesis, and self-assembly of perylene diimide (PDI) based near-IR intracellular probe (PS-PDI). PS-PDI molecules undergo aggregation to form self-assembled nanospheres and nanorods morphology in THF : H2O (1 : 1) and DMSO : H2O (1 : 9), respectively. The nanospheres have an open hole on surface reminiscent of vesicle structure (with a diameter of internal void in the range of 20-25 nm) whereas lengths of the nanorods extended up to few μm range. The Pd0 based depropargylation leads to de-aggregation of these PS-PDI aggregates into smaller spherical aggregates as evidenced by DLS, SEM, and TEM studies. Interestingly, these aggregates of PS-PDI in solution show highly sensitive behavior in the presence of Pd0 showing absorbance changes in NIR region (λmax = 710 nm) and quenching of emission at λem 630 nm (DMSO : H2O, 1 : 9) with a limit of detection = 6.6 × 10-9 M or at λem 564 nm (THF : H2O, 1 : 1) with limit of detection = 2.1 × 10-8 M. Time and concentration dependent kinetics profiles of PS-PDI aggregates revealed an impressive rate constant value of 0.4 s-1 and 0.21 s-1 (DMSO : H2O, 1 : 9), respectively in fluorescence and UV-Vis spectroscopy using 2 × 10-5 M concentration of Pd0. PS-PDI undergoes rapid internalization into HeLa cells with low cytotoxicity and was successfully used as an intracellular imaging reagent for Pd0 in live HeLa cells. For practical applications, we exploited these nano-aggregates of PS-PDI for estimation of Pd2+ in the presence of a NaBH4-PPh3 mixture, Pd0 in drug and environmental samples, and Pd2+ in urine samples with excellent selectivity and sensitivity.