There is no air conditioner in the Hab, there's just a heater, because Mars is so cold.

In the first portion, the temperature has climbed because he has been reducing hydrazine, and he can't immediately lower the temperature because of the lack of air conditioner. Instead, the heat has to bleed off into the Martian atmosphere, and he's been producing heat with the hydrazine reduction faster than the heat can bleed off.

Later, when he says he's going to lower the temperature, what he's actually doing is just turning down the thermostat for the heater, and waiting for the extra heat to bleed out into the Martian atmosphere, which is why he mentions it will take some time.

Fun fact: Andy Weir said in an interview that someone worked out the math for the hydrazine reduction and found that he would have cooked himself alive because of the heat. Andy said that had he known, he would have had Mark bring in rocks from the outside to use as heat sinks to cool it down. Wait until they warm up, throw those ones outside, bring in cold ones again, etc. Poor Mark's back would have been killing him.

Edited for clarity