Aimed to inter-story isolation system, a dynamic analysis equation is established based on non-proportionally damped MDOF model. The seismic ground motion is assumed to be Clough-Penzien model, the pseudo excitation method is used to analyze the random response. The maximum inter-story elastic displacement limit is adopted as the performance index of the structure. The dynamic reliability is calculated using the equivalent normalization method. With a 12-story frame shear wall structure chosen as numerical example, the pseudo excitation method is used to analyze the random dynamic reliability of the inter-story isolation under different design parameters. The results showed that the overall reliability of inter-story isolation structure is significantly higher than that of the non-isolated structure, and increases with the increase of isolation layer stiffness and decreases with the increase of isolation layer damping, the harder the soil of the structural site, the higher the reliability.