This study takes the indoor substation adjacent to the elevated urban train line as the engineering background, investigates the structural vibration response law of the substation induced by the operation of the subway line through on-site vibration measurement, and proposes a novel nonlinear gas-spring quasi-zero stiffness isolator (NGS-QZSI) is proposed to reduce the structural vertical vibration and further reduce the safety distance. The software ABAQUS is used to establish a structure-equipment coupling numerical analysis model considering soil-structure interaction, and its effectiveness and accuracy are validated based on the measured results. The structural vibration response analysis is carried out under different vibration source distances, and a nonlinear gas-spring quasi-zero stiffness isolator is proposed to be employed for substation structural vibration isolation. The research results show that the substation structure under subway load excitation is dominated by vertical vibration, and its vibration response increases gradually with the increase of floor level. When the substation structure is less than 45 m from the subway line, the structural response exceeds the safety limit (12.5 μm/s) of the VC-C standard. With the vibration isolator attached, the structural vibration response is significantly reduced, with the peak and root mean square response controlled by more than 70%. Particularly, the safe distance of the substation from the subway line is reduced from 45 m to 20 m. Moreover, the frequency domain result analysis indicates that the proposed nonlinear vibration isolator can effectively control the low-frequency vibration of the structure.