Base stats are the stats for each Pokemon that are the basis of the final stat count.
Each Pokemon has a base stat that doesn't change e.g. the base stats for a Charmander (or any other Pokemon) are always the same and will be the same for ANY Charmander.
On top of base stats are then IVs, EVs & Nature, all of these together will give your Pokemon it's stats.
So any Pokemon of the same species with the same IVs, EVs & Nature and at the same level will have the same final stats total.
Short answer: They are pre-programmed stats for your Pokemon based on species.