The most common and most likely answer to this crossword clue is the 12 letter word HYPOTHALAMUS
I've seen this crossword clue in The Times
H
Y
P
O
T
H
A
L
A
M
U
S
More clues leading to the result HYPOTHALAMUS
Buddy explains!
The straight part
We know that "temperature controller" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case temperature controller = hypothalamus.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does HYPOTHALAMUS mean?
HYPOTHALAMUS noun- A region of the forebrain located below the thalamus, forming the basal portion of the diencephalon, and functioning to regulate body temperature, some metabolic processes and governing the autonomic nervous system.