Are you trying to see this on a flashing LED or are you using a scope? You're not going to be able to see a multi MHz clock flash on an LED. What frequency is nios_clk? Have you made sure that the pin you assigned SYS_LED[0] in the Pin Planner is configured correctly (maybe needs a pull-up?)?
The led pin is gpio only.nothing is there and test point only. The nios clk is 100mhz, I am using oscilloscope to capture the wave form. A constant one is shown only. Pin assignment is correct. The pll locked is high but nothing came out from the pin
Without seeing a design or code, it's pretty much impossible to help. Can you provide more detail and maybe some code? Also what you've tried so far for debugging.