This research has made it possible to conduct a case study by means of the application of Grey Relational Analysis in order to construct a Balanced Scorecard System (BSC) for the National Museum of Natural Science (NMNS) in the process of a decisive organizational change. The Key Performance Indicators (KPI) for the NMNS prior to and after organizational or structural changes were also investigated. The findings show that: KPI places emphasis on the growth rate of customers and promotion of public relations in the financial perspective in order to enhance customers' satisfaction and improve service quality as evaluated from the customer perspective. Meanwhile, the project highlights senior managers' involvement in the informational technology so that they are able to deal with the applied cases not only from the internal process perspective, but also from employees' professional ability and satisfaction from the learning perspective; A different set of KPI caused by organizational changes deserves further investigations; The findings can serve as an example for the organization to carry BSC into effect.