The father of my children and I live in the same house bbut we are not together and he threatens me he says that I can leave but I can't take the kids with me but he is not on the birth certificate. Can he dod that

No. The fact that he is not on the birth certificate does not change his rights. But it does mean that he will need to go to court to enforce his rights. If you leave with the children, he has not right to prevent it or hold onto them. If he calls the police to prevent your leaving, you show them he is not on the birth certificate.

But he can then file in court to have custody established.

In my area no he cannot do that if he is not on the birth cerificate and you are not married to him.