In view of the high-sensitivity vibration effect of precision instrument laboratory buildings under the influence of surrounding traffic loads, field micro-vibration tests under various working conditions were carried out based on actual projects. Combined with numerical simulation, measured data served as input loads to simulate the vibration effect of various traffic loads on the floor of a building structure, and the structural vibration laws under the comprehensive action of various loads were analyzed. The vibration isolation effect of the isolation ditch on the oblique orthogonal load was investigated according to the corresponding safety index. The results show that the main frequency components of the site vibration frequency caused by various traffic loads are approximately 25 Hz and that the root-mean-square speed value is stable below VC-E, which meets the design requirements. Under the comprehensive action of multiple loads, the site structure will produce a vibration amplification effect, which is obvious when all types of loads are distributed symmetrically and the curve distribution is controlled by load factors with large amplitudes. The isolation effect of a small isolation ditch is best when it is located close to the source and the building. The depth of the isolation ditch must be greater than the maximum depth of the source to achieve better results, and the width has little influence. The effect of a small isolation trench on vertical vibration is poor, and the oblique orthogonal triaxial load has a counteracting effect on the vertical component. Thus, additional structural vibration isolation measures are needed. The research results provide a reference for engineering vibration isolation, damping measures, and structural design.