The heart of a military officer, say (6)
I believe the answer is:
kernel
'the heart' is the definition.
('kernel' can be a synonym of 'heart')
'a military officer say' is the wordplay.
'a military officer' becomes 'colonel' (colonel is a kind of military officer).
'say' shows a homophone (sound like).
'colonel' is a homophone of 'KERNEL'.
'of' acts as a link.
(Other definitions for kernel that I've seen before include "Inner part of nut" , "Nuts and bolts" , "Essence" , "Heart of a nut" , "Essential part" .)