"this device was controlled by PC. Now, I want to design a microprocessor system to execute it."

As it's already running on a PC, why not look at one of the little embedded PC-compatible modules?
eg, PC-104
here's one on a DIMM: http://www.dpie.com/dimmpc/dimmpc386b.html

"About hardware, I don't want to change too much ... How to implement communication between AD convertor"

If you're sticking with the same ADC, then that will define what you need - you will have to read its datasheet, and implement whatever it tells you!
Try visiting the manufacurer's website - they probably have application notes and examples.

Why not stick with the same interface used with your PC?