Polycyclic aromatic hydrocarbons (PAHs) are regarded as promising electrochemiluminescent (ECL) emitters owing to their high quantum efficiency and inexpensive production. Despite the fact that the ECL properties of the pure PAH microcrystal (such as rubrene microcrystals, Rub MCs) have gained extensive attention, it is a challenge in controlling the morphology and size to reduce the inner filter effect. Herein, an advanced ECL emitter of palladium nanoparticle-functionalized hollow PAH-metal nanocubes was prepared by an in situ redox deposition method (the resultant nanocomposites were abbreviated as Pd-Rub-Ag@Au nanocubes). Specifically, the rubrene-decorated Ag@Au nanocubes (Rub-Ag@Au nanocubes) were prepared using the Ag@Au nanocubes as a template and a rubrene cation radical (Rub•+) as a reductant, and then Pd nanoparticles (Pd NPs) were in situ reduced on the surface of Rub-Ag@Au nanocubes. Impressively, compared with the Rub MCs, Pd-Rub-Ag@Au nanocubes showed uniform size and significantly enhanced ECL efficiency and intensity in the aqueous media. As a proof-of-concept, the Pd-Rub-Ag@Au nanocube-based ECL biosensing platform combined with a multisite-anchored DNA nanomachine was constructed for ochratoxin A (OTA, a type of mycotoxin) detection. The DNA nanomachine covered with high-density recognizing sequences could operate toehold-mediated strand displacement amplification on the sensing platform and promote the movement efficiency and velocity greatly. Due to the advanced performance of Pd-Rub-Ag@Au nanocubes and high recognition efficiency of the DNA nanomachine, the proposed biosensor for OTA detection can achieve a detection limit of 4.7 fg/mL ranging from 0.01 to 100 pg/mL, which offers an ingenious method for the further application of PAHs.