Considering the output of shaking table is not a kind of absolutely uniform base excitation in vibration test， some unexpected response behavior could be occurred. With the research of theoretical analysis， numerical simulation and experiment confirmation based on mode superposition theory， the output response of shaking table is decomposed in mode space， then the non-uniform base excitation is characterized and quantified. Furthermore， with the experiment data analysis of empty mesa， axis vibration and transverse vibration test of typical structure， the non-uniform base excitation is quantified from two aspects of response power spectrum and root mean sqaure. Theoretical and experimental results indicated that the existed non-uniform base excitation can be caused by two important factors including the elastic support between armature and table top， and the symmetry of test structure are two important factors that could cause the non-uniform output of shaking table.