In the big data era, business applications generate huge volumes of data, making it extremely challenging to store and manage those data. One possible solution adopted in previous database systems is to employ some types of encoding techniques, which can effectively reduce the size of data and consequential improve the query performance. However, existing encoding approaches still cannot make a good tradeoff between the compression ratio, importing time and query performance. In this paper, to address the problem, we propose a new encoding-based database system, HEGA-STORE, which adopts the hybrid row-oriented and column-oriented storage model. In HEGA-STORE, we design a GPU-assistant encoding scheme by combining the rule-based encoding and conventional compression algorithms. By exploiting the computation power of GPU, we efficiently improve the performance of encoding and decoding algorithms. To evaluate the performance of HEGA-STORE, it is deployed in Netease to support log analysis. We compare HEGA-STORE with other database systems and the results show that HEGA-STORE can provide better performance for data import and query processing. It is a much compact encoding database for big data applications.