Programming

The assembly code generated by assembler, from a C-source code depends on the CPU architecture underlying it, eg x-86 . Then does the assembler output of a simple C-source code (containing common function-calls of both windows and linux) differ between Operating Systems ?

Yes, it can. One reason is the structure/symbol nomenclature of runtime libraries. Another reason is entry points (names) for system calls are not prescribed by any standard, so they could be almost any name the kernel designer decides to use.

This assumes you meant for example, windoze vs unix vs xenix or something like that.
The differences between Linux Suse and Ubuntu, which I have looked at, are minimal.

One thing that can radically change the assembler code, even for the same OS and identical code, is the optimization level. Loop unrolling for example.