Lets start with what atoms are. Atoms are (besides quarks) the tiniest things that make up every supstance in the universe, including molecules.
On the other hand, elements are supstances that cannot be broken down into other supstances. Some elements are Hydrogen, Oxygen, Lithium...
Molecules are made up out of different elements. For example, H2O (water) is made out of Hydrogen and Oxygen. All of these things are made up of atoms.