Aqueous zinc batteries (ZBs) attract increasing attention for potential applications in modern wearable and implantable devices due to their safety and stability. However, challenges associated with biosafety designs and intrinsic electrochemistry of ZBs emerge when moving to practice, especially for biomedical devices. Here, we propose a green and programmable electro-crosslinking strategy to in-situ prepare a multi-layer hierarchical Zn-alginate polymer electrolyte (Zn-Alg) via the superionic binds between the carboxylate groups and Zn2+. Consequently, Zn-Alg electrolyte provides high reversibility of 99.65% coulombic efficiency, over 500 h long-time stability, and high biocompatibility (no damage to gastric and duodenal mucosa) in the body. A wire-shaped Zn/Zn-Alg/α-MnO2 full battery affords 95% capacity retention after 100 cycles at 1 A g−1 and good flexibility. The new strategy has three prominent advantages over the conventional methods: (1) the cross-linking process for the synthesis of electrolytes avoids the introduction of any chemical reagents or initiators; (2) a highly reversible Zn battery is easily provided from a micrometer to large scales through automatic programmable functions; and (3) high biocompatibility is capable of implanted and bio-integrated devices to ensure the body safety.