Abstract Self‐powered biosensors (SPBs) based on biofuel cells (BFCs) use electrical output as a sensing signal without the need of external power supplies, providing a feasible approach to constructing miniaturized implantable or portable devices. In this work, a novel nanozyme of gold nanoclusters/palladium nanocubes (AuNCs/PdNCs) heterostructure is successfully fabricated to develop an innovatively self‐powered and non‐enzymatic glucose sensing system. The AuNCs/PdNCs with glucose oxidase (GOD)‐like activity exhibits superior electrocatalytic and non‐enzymatic sensing performance toward glucose. The non‐enzymatic BFCs‐based SPBs system, established on the AuNCs/PdNCs (anodic catalyst) and single atomic Fe sites coupled with carbon‐encapsulated Fe 3 C crystals (Fe 3 C@C‐Fe SACs as a cathodic catalyst) platform, exhibits an exceptional sensitivity to glucose with 0.151 µW cm −2 m m −1 (3.4 times higher than the PdNCs), outstanding selectivity and robust stability. The outstanding performance of the BFCs‐based SPBs system can be attributed to the synergistic cooperation between the PdNCs and AuNCs.