According to the TRM, the SIO pins can withstand 5V even with lower Vddio. But you cannot use them as analog input pins. So you need to select 'digital high-Z' as input mode (no pull-up since this would pull Vusb to Vdd) and configure a proper reference voltage for the pin.
But you still should include input protection nonetheless, since USB is an external connector and one never knows whats happening there...
Hi ,I had been use the VBUS monitor function before but that was been unstable?? I didn't mention about the connection of this SIO pin, HaHa. Anyway according the data sheet, Electrical specifications of SIO is Vssd–0.5 to 6V, so that OK to connect +5v pin, regardless CPU has use +3v supply, But you shouldn't be connect to D+- pin, because D+- is high speed and sensitive. I think you rather use isolated USB for protect all stuff. Thank you.