The term Shear Transformation Zone (STZ) refers to the atomic cluster that dissipates external stress through cooperative shear. The STZ is the process that describes the local atomic rearrangement mechanism of metallic glasses (MGs). Based on the cooperative shear model (CSM), the size of an STZ has been estimated using the rate jump method (RJM), nano-scale creep method (NCM), first pop-in statistical method (FSM) and serration-flow statistic method (SSM), respectively. In the nanoindentation process, different sizes of STZs can be elicited by employing different experimental conditions (indentation depth and loading rate). In addition, different characterization methods exhibit various degrees of response to changes in the experimental conditions. In order to study the heterogeneity of the STZ of MGs using different nanoindentation methods, in this study, three types of Zr-based MGs with different Poisson's ratios were used as the research objects, and the sizes of the STZs of these amorphous alloys were calculated using the previously mentioned methods. By applying different maximum loads and loading rates, the effect of the nanoindentation test parameters on the size of the metallic glasses' STZs were characterized using different nanoindentation methods. Under the same testing conditions, the volume of the STZs was calculated using each method that exhibited improvement with the increase of the Poisson's ratio. The calculated results obtained using the RJM, NCM and SSM were found to be much greater than those obtained using the FSM. With the increase in the loading rate, the results obtained using NCM decreased, whereas the statistic method results slightly increased. At the maximum load, the STZ volume calculated using the JRM, NCM and SSM increased significantly. The FSM was not affected by the maximum load. Finally, these differences are discussed from the aspects of the calculation principles and the activation and evolution of the STZ.