The invention discloses an environmental sensitive area database construction method based on a GIS system, and a server. The method is completed in the server, and comprises: obtaining environmental sensitive area thematic data and storing the data into a map table; distributing a unique ID for each environmental sensitive area in the map table, and correlating the environmental sensitive area thematic data with the IDs; according to the number of the environmental sensitive areas, diving the map table into map layer tables in the same number, each map layer table being related to one ID and corresponding to one environmental sensitive area, and finally establishing an environmental sensitive area database, each map layer table being stored with basic attribute information and geographical location information of the corresponding environmental sensitive areas, and after the data in each map layer table is called by a client, the data is used to display map information of the corresponding environmental sensitive area. The environmental sensitive area database constructed by the method contains real-time updates and expansions of environmental sensitive area distribution.