No. Google pay will not work with MIUI if you have an unlocked bootloader. I just ran into this issue and contacted google support.
Their official response is as follows:
"
I had escalated your case to our specialist team, I have received an updated. Our specialist found that your device bootloader is unlocked. I request you to please have the device bootloader locked. In order to use the Google pay app for the in-store purchase, the bootloader of the device needs to be blocked and also should have the NFC enabled on the device. Also make sure the Google pay is set as a default payment app. Please contact the device manufacturer to have the bootloader locked.
"
So in order to use Google Pay we either have to able to find a way to relock the bootload while keeping the system functional, or find a way to block google from detecting the unlocked bootloader.