first:
In an application, I have to have a large size of data array (with each element containing 6 bytes) in code section. In C we can say that i wanted to have,
char LargeArray[1000][6];
Ok, forget 1000, but keep large

But i ran out of code space so, i turn to 89C4051, but at this time my program grows upto 3701 Byte. And i have to add many things in it.

So you have to "add many things" in 400 bytes and have a "large" array as well.
why are we discussing compression, there is no way in hades you will get by with in with your current processor.

Go get a processor with 64k flash, there is so many of them, and get this thing going.

As I have stated twice already, you will get in speed trouble, so get a fast one e.g. Cygnal.

Erik