Why my Nios II run slowly ?

Count the instructions in the loop:

1) Read of LED_TOGGLE for the io_write

2) Write of LED_TOGGLE to the hardware

3) Read of LED_TOGGLE for the invert

4) the invert inself

5) Write back of LED_TOGGLE

6) Unconditional branch

IIRC a nios/e takes 5 clocks per instruction - so that is at least 30 clocks.

The constant LED_PIO_DATA_BASE might also be created each loop iteration.

Add in any extra clocks for the avalon write caused by your slave itself.

Make LED_TOGGLE a local variable (so it can be assigned to a register).

Compile with -O2 so that the compiler moves some calculations outside the loop.

That should get you to a three instruction loop.