The invention discloses an indexing method of a distributed column storage system. The method comprises the steps of obtaining distribution characteristics of each column of data, and setting a domain value and a division rule of each column of data; obtaining a continuous data area after division according to the domain value and the division rule; establishing an area coding vector corresponding to each data area; performing statistic calculation to obtain statistic information of each column of data, and combining the statistic information with the corresponding area coding vector to obtain an area coding vector with the statistic information; and performing data indexing by taking the area coding vector with the statistic information as a bit vector of a bitmap index. According to the indexing method of the distributed column storage system, a division mode of the grouping bitmap index conforms to a query filtering condition by setting the domain value and the division rule of each column of data; and by calculating the statistic information of the column data, the accuracy of grouping bitmap query is improved, the statistic information of the data in the column storage system can be reserved, and the integrity of data information is ensured.