Zinc-ion capacitors (ZICs) are viewed as a promising energy storage solution for portable electronics and biocompatible devices. Nevertheless, current ZICs technology faces challenges such as restricted specific capacitance, suboptimal cycling performance, and ongoing validation efforts regarding their biocompatibility. Herein, hierarchical porous carbon materials were prepared through a two-step carbonization-activation method using kapok fiber biomass as the precursor. The kapok fibers-based cathodes contain abundant micropores and mesopores, which provide abundant active sites for Zn2+ storage and optimize reaction kinetics. The ZICs demonstrate an ultra-high cycling life exceeding 240,000 cycles. Meanwhile, theoretical calculations verify that large micropores exhibit a reduced diffusion energy barrier for [Zn(H2O)6]2+, which accelerates [Zn(H2O)6]2+ adsorption/desorption and increases the available reversible capacitance. Furthermore, the ZICs exhibit excellent biodegradability in soil, simulated human body fluids and real seawater, and low cytotoxicity to human cells and minimal tissue damage in animal. This research presents a potential pathway for the advancement and verification of biocompatible ZICs, thereby contributing to their prospective practical utilization in biomedical and environmental field.