Johari-Goldstein or b relaxation, persisting down to glassy state from a supercooled liquid, is a universal phenomenon of glassy dynamics. Nevertheless, the underlying micromechanisms leading to the relaxation are still in debate despite great efforts devoted to this problem for decades. Here we report experimental evidence on the structural origins of Johari-Goldstein relaxation in an ultra-quenched metallic glass. The measured activation energy of the relaxation (B26 times of the product of gas constant and glass transition temperature) is consistent with the dynamic characteristics of Johari-Goldstein relaxation. Synchrotron X-ray investigations demonstrate that the relaxation originates from short-range collective rearrangements of large solvent atoms, which can be realized by local cooperative bonding switch. Our observations provide experimental insights into the atomic mechanisms of Johari-Goldstein relaxation and will be helpful in understanding the low-temperature dynamics and properties of metallic glasses.