Aqueous supramolecular long-lived near-infrared (NIR) material is highly attractive but still remains great challenge. Herein, we report cucurbit[8]uril confinement-based secondary coassembly for achieving NIR phosphorescence energy transfer in water, which is fabricated from dicationic dodecyl-chain-bridged 4-(4-bromophenyl)-pyridine derivative (G), cucurbit[8]uril (CB[8]), and polyelectrolyte poly(4-styrene-sulfonic sodium) (PSS) via the hierarchical confinement strategy. As compared to the dumbbell-shaped G, the formation of unprecedented linear polypseudorotaxane G⊂CB [8] with nanofiber morphology engenders an emerging phosphorescent emission at 510 nm due to the macrocyclic confinement effect. Moreover, benefiting from the following secondary assembly confinement, such tight polypseudorotaxane G⊂CB[8] can further assemble with anionic polyelectrolyte PSS to yield uniform spherical nanoparticle, thereby significantly strengthening phosphorescence performance with an extended lifetime (i.e., 2.39 ms, c.f., 45.0 μs). Subsequently, the organic dye Rhodamine 800 serving as energy acceptor can be slightly doped into the polyelectrolyte assembly, which enables the occurrence of efficient phosphorescence energy transfer process with efficiency up to 80.1% at a high donor/acceptor ratio, and concurrently endows the final system with red-shifted and long-lived NIR emission (710 nm). Ultimately, the as-prepared assembly is successfully exploited as versatile imaging agent for NIR window labeling and detecting in living cells.