Description
No, VCC_CLKIN and VCCIO do not need to be connected to the same voltage levels in Cyclone® IV devices.
For example, the VCC_CLKIN can be powered with 2.5V while the VCCIO is powered with 3.3V for the same I/O bank.
Refer to High Speed I/O Standards Support in I/O Features in Cyclone IV Devices (PDF) for further information.