It is an intriguing and urgent goal to quantitatively or semi-quantitatively unveil the correlation between the properties and the microstructure for metallic glasses. The relationship between the microstructure and mechanical property of three Zr-based bulk metallic glasses (BMGs) were investigated. The results show that three BMGs have similar XRD patterns, crystallization behavior and comparable relaxation enthalpy. The precipitated phases of three fully crystallized BMGs are Zr6Al2Ni-type and CuZr2-type phases. The content of CuZr2-type phase increases but that of Zr6Al2Ni-type phase decreases with increasing Zr content. A remarkable discrepancy in plastic flow behavior in compression and nanoindentation tests originates from the different contents of CuZr2-type cluster named as the geometrically unfavorable motifs (GUMs). The plastic flow stress and strain decrease while the plasticity increases with increasing fraction of CuZr2-type cluster. The fitting parameters from cumulative probability statistics are fingerprints for investigating the plastic flow and plasticity of the BMGs, and would be a valuable clue for developing the BMGs with good plasticity. The mechanism of correlation between the GUMs and the plasticity was also discussed. This work would provide a favorable route for discovering the quantitatively correlation between the GUMs and the plasticity in the BMGs.