If your Google Pay setup is telling you that your phone is rooted or altered in some other way, then check the following:
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Make sure all your apps are updated. Goto play store app > your profile icon > My apps and devices > Update all apps. After all apps are updated, try again. Uninstall Google Pay, reboot, reinstall Google Pay if need be.
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Make sure your bootloader is locked. If your phone shows “Orange state” at bootup time, then your bootloader is unlocked and needs to be locked.
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You need to be running certified builds. Lineage or eOS or any other custom rom will not support Google Pay.
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Install this SafetyNet test app from Play store and run it. It should say “Passed”. If not, there is something wrong with your build (2 and 3 above).