If I do a factory reset, will the original operating system come back?

I have a Galaxy J3 that Andriod updated 2 days ago. I am not getting many notifications, and the notifications are sporadic. I do not like this update, and want to go back. I am willing to have to re-install apps if necessary.

It will not roll back to the prior version of the OS, but it may still fix your problem by resetting everything back to a stock state. It's not unheard of for an update to have a glitch that requires a reset, and some people do it anyway after any OS update.

If you do go ahead with the reset, just make sure you remember your Google account info, because it may ask for it during the setup process depending on how you initiated the factory reset.

And you will lose all your data, pictures, music, etc.

If you want to go back to the previous version of the OS, you'll have to reflash that - see [Samsung] How to flash Stock ROM via ODIN.