Waveshare USB3300 board with stm32f429
The schematic you linked shows that the USB3300 expects a 3v supply for its onboard electronics (and 3v level signalling for its IO pins), and a 5v supply for the USB port, which is controlled by a load switch. For proper functionality connecting to a USB device, you need to connect a 3v supply with enough power for the onboard electronics, and a 5v supply with enough power for whatever USB device you attach.