Although microenvironments surrounding single-atom catalysts (SACs) have been widely demonstrated to have a remarkable effect on their catalytic performances, it remains unclear whether the local structure beyond the secondary coordination shells works as well or not. Herein, we employed a series of metal-organic frameworks (MOFs) with well-defined and tunable second-beyond coordination spheres as model SAC electrocatalysts to discuss the influence of long-distance structure on the ammonia synthesis from nitrate, which were synthesized and denoted as Cu12-NDI-X (X = NMe2, H, F). It is first experimentally confirmed that the remote substitution of function groups beyond the secondary coordination sphere can remarkably affect the activity of ammonia synthesis. Meanwhile, the -H endowed Cu12-NND-H exhibits a superior ammonia yield (35.1 mg·h-1·mgcat-1) and FE (98.7%) to those modified with -NMe2 and -F, which also shows good stability at 100 mA·cm-2. The remarkable promotion of the modulated second-beyond coordination structure is unraveled to result from the adjustable d-band center of the Cu active site leading to promoted adsorption of the NO3- and protonation of key intermediates. Encouraged by its extraordinary ammonia yield, we employed the Cu12-NND-H electrode as a cathode to assemble one rechargeable Zn-nitrate battery that exhibits an impressive power density of 34.0 mW·cm-2, demonstrating its promising application in energy conversion and storage.