This paper studies the seismic and micro vibrations of the high-tech factory with and without lead rubber bearings (LRBs) using the three-dimensional (3D) finite element analysis. The soil-structure interaction is included using the p-y, t-z, and Q-z nonlinear soil springs, while the time-history analysis is performed under seismic, wind, or moving crane loads. The finite element results indicate that the moving crane does not change the major ambient vibrations of the factory with and without LRBs. For a normal design of LRBs, the high-tech factory with LRBs can decrease the seismic base shear efficiently but will have a much larger wind-induced vibration than that without LRBs, especially for the reinforced concrete level. Because micro-vibration is a major concern for high-tech factories, one should use LRBs with a large initial stiffness to resist wind loads, and use a small final LRB stiffness to reduce the seismic load of high-tech factories. This situation may make it difficult to obtain a suitable LRB, but it is an opportunity to reduce the seismic response without increasing the micro-vibration of high-tech factories.