I am having some source which will compile very well in linux 2.4 kernel
but when i want to compile that in linux-2.6 with suitable change in makefile ,i have also included the flags needed for 2.6 kernel but when i copile it give error in header file as in iqr.h irq_vector.h is not there and also huge number of errors w.r.to header file.If anybody is having idea please let me know.

The reason is simple. What I understand is; any code that is very specific to a particular kernel and uses kernel headers, may work across different kernels if the implementation does not differ across these kernels. Since 2.4 and 2.6 supports same gcc version hence this is not a problem here.

You have mentioned about irq.h. The implementation of irq handling differs a significantly between 2.4 and 2.6. In kernel 2.6 the architecture dependent code and and architecture independent code are separated. If you want your code to be used with kernel 2.6 you will have to make changes in you code for 2.6.

What the error i am getting is in

<asm/irq.h> file contains
the line
#include "irq_vectors.h"
when I compiled it is telling that no such file called iqr_vector.h is not there ,how change in my source will resolve this problem.

With a quick search I found that the file "irq_vectors.h" is with kernal 2.6 and not with 2.4. As I all ready mention this is a part of architecture dependent code. But I am surprise as you told that your code compiles on 2.4 and not 2.6.

Yes, I told that if you want your code to be used with kernel 2.6 you will have to make changes, but this is not as simple as I said. irq_vectors are used by 2.4 as well, but I did not find any "irq_vectors.h" with 2.4, it is there with 2.6. I think it is similar(may not be same) as hw_irq.h in 2.4 which is the architecture dependent code.(note that replacing it will not work)
I tried to answer you questions, still I can help more provided I have some knowledge about your code. You actually need to have a in depth look into the two implementations to make you code change. I am sorry to put it very simply, but its not that simple to do it.