Abstract: The high pile frame structure with characteristics of high hanging pile foundation and low lateral stiffness is usually applied in the design of cross-reservoir buildings. It is easily deformed and vibrated under the change of external environment, which affects the normal operation of the project. In view of the micro-deformation and micro-vibration of high pile frame structure, a method of adding soil protection outside pile foundation was proposed for control. Taking the high pile frame structure of a scientific apparatus project as an example, the finite element method was used to analyze the vibration characteristics of the overall structure, micro-deformation under temperature load, micro-vibration during the passage of high speed rail, and displacement response subjected to wave load under two design schemes respectively: the high-pile frame scheme and the high-pile frame + soil protection scheme. The numerical analysis shows that the high-pile frame + soil protection scheme can reduce the high-order natural vibration frequencies of the pile foundation system, and avoid the resonance risk. Additionally, it can effectively control the micro-deformation caused by temperature change and the micro-vibration caused by the high speed rail within the allowable range of the project, and greatly reduce the horizontal deformation of the pile foundation system under wave load. Therefore, setting soil protection outside pile foundation can effectively control the micro-deformation and micro-vibration of the high pile frame structure, which is an economical and efficient vibration control scheme.