Heartless spy sat on space organisation (6)
I believe the answer is:
system
'organisation' is the definition.
(synonyms)
'heartless spy sat on space' is the wordplay.
'heartless' suggests removing the centre.
'sat on space' becomes 'stem' (I am not sure about this - if you are sure you should believe this answer much more).
'spy' with its middle taken out is 'sy'.
'sy'+'stem'='SYSTEM'
Can you help me to learn more?
(Other definitions for system that I've seen before include "Group of elements forming a unified whole" , "Routine" , "Way" , "Method of organisation" , "Set of things in a connected whole" .)