This study empirically investigated the changes of performance evaluation systems under the environment of supply-chain e-commerce. The objectives of e-commerce include obtaining financial profit, internal innovation through processes integration, learning with information flow, and customer satisfaction through quick response. These objectives are generally consistent with the four evaluation measures of balanced scorecard(BSC). This study, first, demonstrated that perceived environmental uncertainty(PEU) has a significant effect on the adoptions of e-commerce and BSC, and severe competition positively influences the use of e-commerce. With cluster analysis and subgroup analysis, we also showed that under the high adoption levels of e-commerce, the high utilization of BSC can improve the supply-chain performance of a firm. In addition, it was found that the use of e-commerce indirectly and significantly affects supply-chain performance through inter-organizational information flow, and the supply-chain performance of a firm leads to the improvement of organizational performance.