I accidentally paid a $1000 to the app store, how can I withdraw it?

I'm not aware of a way to retrieve money that you added to your Apple ID.

Speak directly to Apple for further help.

Get Support -

https://getsupport.apple.com/

M1 Mac mini, macOS 11.4; Watch, series 5 GPS/cellular, watchOS 7.5; iPad Pro 2nd Gen, iPadOS 14.6; iPad Air 2, iPadOS 14.6; iPhone 12 Pro, iOS 14.6; TV 4th Gen, tvOS 14.6  HomePods, audioOS 14.6 and Airport Express w/ Airplay 2

You don't provide much information!

Did you place $1000 in Apple Cash?

Transfer it to a bank

https://support.apple.com/en-us/HT207882

M1 Mac mini, macOS 11.4; Watch, series 5 GPS/cellular, watchOS 7.5; iPad Pro 2nd Gen, iPadOS 14.6; iPad Air 2, iPadOS 14.6; iPhone 12 Pro, iOS 14.6; TV 4th Gen, tvOS 14.6  HomePods, audioOS 14.6 and Airport Express w/ Airplay 2