HMRC will find out about the rental income split from your tax return, that needs to be filed online by the 31st January every year, for the previous year ending the 5th April. If you are married, jointly own a property and share rental income in unequal shares, then you must file a deed and a Form 17 tax declaration to HMRC.
If you fail to file a Form 17 with a deed, then HMRC will reverse your declaration and you'll be liable for tax on an equal share of the rental income. Read more here - Form 17 Income Tax Declaration for Married Couples.