I am a beginner of Electronics
I am going to control lots of I/O. it is about 1,000.
Then get serious. You don't just scale up electronics by adding extra parts lots of other things come into effect when you scale things up. Anything.
Say you want to make a car, but make it 300 ft tall. If you just took the car design and scaled up each part it would collapse when you put it together because of the weight / strength ratio of the steel.
Just like this once you have a stupid number of I/Os lots of other things come into play like power supply smoothing, interference, layout, decoupling and lots of things you probably have never heard of.
So get serious, learn some electronics, make some projects even 100 times smaller and learn some skills. Then you might think about such a mammoth project.
However this sounds like an X-Y Problem what exactly do you want to make that requires such a lot of I/O.