My ex owes back child support and I just found out today he filed will they will they automatically take it out or will he have to notify them that he did his taxes

Does he want them to take it out?

It depends. Usually, the Child Support has a precedence and the IRS will take his refund (the amount he owes) to cover it. In certain situations the IRS can release the refund for the child support, but it will not happen automatically. 

Here's a link to the Treasury Offset Program with more information: https://www.treasury.gov/services/report-fwa/Pages/treasury_offset_program.aspx