The upper atmosphere is hot. It’s been heated by the Sun and reaches thousands of degrees.
The lower layers of the atmosphere are cold. You’re probably thinking of being at sea level and then going up a mountain. That’s still low in the atmosphere.
The difference between the top of a mountain and the ground towards sea level is that the lower atmosphere is mostly heated by the ground. The Sun warms up the ground and the ground then heats up the air it’s in contact with.
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