why software's speed is so slowly run on nios II

A statement like a=3 takes one cycle to execute on the Nios II/f assuming the instruction is in the cache.

Are you familiar with the operation of caches? Also, what signals are you observing in signaltap to see the

instructions flow down the pipeline? If you only look at the Avalon instruction master, you'll only see instruction

cache line fills, not instruction execution.

If you post more of your program (maybe a portion of the hot loop), we can give you more information.