The Goddess Flower is an item that you will get early on in need to summon the Harvest Goddess.You summon the Goddess by dropping a Goddess Flower in water. Once she despawns she will drop the flower in case you need her again.
To create it you must make 2 holes and fill them with water, put flowers next to them a pot with a flower in the middle and right-click the pot with a stick multiple times.(See Harvest Goddess). The instructions are also detailed in the "Guide on how to summon Harvest Goddess" book that you get when you start.
Later you can build a Goddess Pond which you can also drop the flower in.