The supramolecular packing mode of organic π-conjugated molecules in the solid state plays a crucial role in determination of the resulting material properties and functionalities. Control and understanding of supramolecular packing of individual building blocks constitute an important step toward optoelectronic and biomedicine. In this work, we have designed and synthesized a series of bis(pyrene) derivatives, i.e., BP1–BP4 with 1,3-dicarbonyl, pyridine-2,6-dicarbonyl, oxaloyl and benzene-1,4-dicarbonyl as linkers, respectively. In solution, all compounds showed low fluorescence quantum yields (Φ < 1.7%) in variable organic solvents due to the twisted intramolecular charge transfer (TICT). In a sharp contrast, BP1 and BP2 in the solid state were self-assembled to form J-type aggregates with almost 30-fold fluorescence enhancement (Φ was up to 32.6%) compared to that in solution. Nevertheless, H-type aggregates of BP3 and BP4 were observed with poor emissive efficiencies (Φ < 3.1%). The proposed molecular aggregates types were confirmed by powder X-ray patterns and single crystal structures. The slipping angles of adjacent molecules of J-type aggregates were 41.07–44.58°, which were smaller than that (64.58–68.45°) in H-type aggregates. Subsequently, B3LYP/6-31G quantum chemistry calculation was performed and the results indicated that the excimeric emission of BP1–BP4 aggregates was closely related to their molecular packing orientation and parameters. Furthermore, the morphologies of supramolecular aggregates based on BP1–BP4 were observed by transmission electron microscope (TEM) and the results showed that BP1 and BP2 were dot-shape nanoaggregates with 2–6 nm in diameters, while BP3 and BP4 showed sheet-like morphologies with 5–10 nm in width and 20–100 nm in length. The nanoaggregates of BP1 and BP2 coated with F108 surfactants showed good pH and photostability in physiological condition. Finally, the nanoaggregates of BP1 and BP2 were successfully employed as fluorescence nanoprobes for lysosome-targeted imaging in living cells with negligible cytotoxicity.