The seed decides how your world is generated. You can only change it for a world that has not been generated yet, so changing it means deleting your current world.

Steps

1. Stop the server completely.
2. Open the Files tab and delete world, world_nether and world_the_end. If your world has a different name, check level-name in server.properties.
3. Open server.properties.
4. Set the seed with no spaces around the equals sign, for example level-seed=104764939073902 or level-seed=mycoolseed.
5. Save the file and start the server. The first start takes longer while the new world generates.

If it did not work

• Same terrain as before: the old world folder still exists. Stop the server and delete it.
• Nether or End look unchanged: delete their folders too.
• The seed went back to the old one: you edited the file while the server was running. Stop first, then edit.

To keep a world but wipe only the Nether, see Reset the Nether.