With increasingly volatile market conditions and rapid product innovations, operational decision-making for large-scale systems entails solving thousands of problems with limited data. Data aggregation is proposed to combine the data across problems to improve the decisions obtained by solving those problems individually. We propose a novel cluster-based Shrunken-SAA approach that can exploit the cluster structure among problems when implementing the data aggregation approaches. We prove that, as the number of problems grows, leveraging the given cluster structure among problems yields additional benefits over the data aggregation approaches that neglect such structure. When the cluster structure is unknown, we show that unveiling the cluster structure, even at the cost of a few data points, can be beneficial, especially when the distance between clusters of problems is substantial. Our proposed approach can be extended to general cost functions under mild conditions. When the number of problems gets large, the optimality gap of our proposed approach decreases exponentially in the distance between the clusters. We explore the performance of the proposed approach through the application of managing newsvendor systems via numerical experiments. We investigate the impacts of distance metrics between problem instances on the performance of the cluster-based Shrunken-SAA approach with synthetic data. We further validate our proposed approach with real data and highlight the advantages of cluster-based data aggregation, especially in the small-data large-scale regime, compared to the existing approaches.