I have a question with regards to overheating with my 2004 Lexus ES 330. When first starting up, both the top and bottom radiator hoses are cool to the touch. Once the car reaches operating temperature, the top hoses gets really hot and the bottom radiator hose is still cool to the touch.

I understand the flow of hot coolant to the radiator when the thermostat is connected to the top radiator hose but I'm confused as to the flow when the thermostat is connected to the bottom radiator hose. How does the flow work? Does it still flow the same way? Or does it flow in opposite direction? I would imagine that the flow would be from the bottom hose up to the top since the thermostat controls the flow of coolant from the engine to the radiator. If that's the case, is it safe to assume that my issue is a bad thermostat since the bottom hose remains cold? How is it that the top hose gets hot and the bottom hose remains cold when the thermostat is connected to the bottom hose?

 

IIRC the 1MZ and 3MZ have a "reverse" cooling system. We can get into the theory but your problem sounds like air lock/trapped air problem or possibly low on coolant. Do the fans operate normally? It is possible the thermostat has failed but they rarely go bad and fail closed it is most often the opposite, engine runs too cool.

If the thermostat is not Toyota genuine then replace it with the proper part.

Go to page 14 of the pdf it shows coolant flow.

 

Last year my 2002 was overheating at stoplights, Then drive and normal. It got worse but the coolant levels looked ok. I am no mechanics but what I did worked. I did check coolant level but I tried adding coolant anyways.
. I solved issue by replacing radiator cap with brand new one. There were no visible leaks I added coolant to radiator directly with engine running and it sucked in about 2 quarts. Next day I did same thing but added a very little bit more. Problem solved and needle stays in center on temp. guage. That was ten thousand miles ago. All good still!