Hi Yusheng,
Both the EMIF16 on the C6678 and the GPIF II on the Cypress FX3 USB controller are programmable. The chances are that you should be able to program the two interfaces to communicate. The IP voltage for GPIF II can be configured for 1.8V so no external voltage translation is needed. Detail on programming the EMIF16 can be found in the External Memory Interface (EMIF16) for KeyStone Devices User's Guide. You will have to contact Cypress for details on configuring the GPIF II interface in the FX3 USB controller. We don't have a reference design for this connection.
Regards, Bill