I recently started a retail store and I am running the business in a building owned by my real estate LLC company. Is there any tax benefits from my retail store paying a higher or lower rent?

An LLC to LLC owned by the same person is like handing money from your left hand to your right hand and thinking you made it lost money.

Yes there is. Your renting might not be considered a trade or business’s on it own to qualify for 20% 199A deduction added by the tax reform. But, you can bring the rental into the trade or business category because you are owner on both end. Being said that, with the rents structuring, you can play with rents to optimize 20% deduction. How do you do that? You probably will not do it yourself and will have to seek out help from tax professionals. Also, you can kind of optimize your non-passive loss from the rental with self- rental recharacterization rule under sec 469.

You're also getting some asset protection benefits. If your retail business hurts somebody, but doesn't own the building, your building should have some protections in a lawsuit or creditor problems. The reverse is also true.

@Jray Randall If you want to generate some earned income from a salary from your business you will lower the rent, if you want more passive income you would increase the rent.