In recent years, spatial applications have become more and more important in both scientific research and industry. Spatial query processing is the fundamental functioning component to support spatial applications. However, the state-of-the-art techniques of spatial query processing are facing significant challenges as the data expand and user accesses increase. In this paper we propose and implement a novel scheme (named VegaGiStore) to provide efficient spatial query processing over big spatial data and numerous concurrent user queries. Firstly, a geography-aware approach is proposed to organize spatial data in terms of geographic proximity, and this approach can achieve high aggregate I/O throughput. Secondly, in order to improve data retrieval efficiency, we design a two-tier distributed spatial index for efficient pruning of the search space. Thirdly, we propose an "indexing + MapReduce'' data processing architecture to improve the computation capability of spatial query. Performance evaluations of the real-deployed VegaGiStore system confirm its effectiveness.