In the era of large data, the data has the characteristics of large volume, obvious spatio-temporal complexity, high real-time requirement, and etc. However, the traditional method of indexing large-scale spatio-temporal data based on tree structure has the problem of low utilization of storage space and low efficiency of query. In order to solve this problem, a new method named HDL-index was proposed to establish the spatio-temporal index based on the distribution of data and historical query records. On the one hand, the whole area was partitioned based on the spatial distribution of the data. On the other hand, taking into account the continuity of query, the query-models were obtained after density-based clustering on historical query objects, and then based on the model coordinates and query granularity of the overall query area segmentation, the two indexes were merged based on their GeoHash codes, and finally the optimal index coding was obtained. HDL-index takes better account of the data distribution and users' queries, making the index on the frequent query area more refined. Compared with the efficiency of the similar method, the efficiency of the index creation is improved by 50%, and the query efficiency of the hotspot region can be increased by more than 75% when the data is evenly distributed in the real aeronautical data set.