More precisely, a
chemical or set of chemicals extracted from a
natural substance, usually a plant or animal without any chemical modification. If the
chemical structure is changed, it's probably then an
artificial flavor, although there's probably some leeway here--for instance, something like
liquid smoke is a natural flavor, even though you have to
burn the wood to get it, which is a
chemical change.
Contrast with artificial flavor which is most likely some sort of petrochemical made to simulate the chemical structure of a natural flavor.