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.
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
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?)?