。
She'll realize what I really meant later on.
Literal
She [topic-は] later me 's true-intent [in-に] will-notice [probably-でしょう].
気づく ('to notice, realize, become aware of') takes the thing realized with に: '~に気づく' ('notice X'). 真意 ('true intent, real meaning') is a Sino-Japanese compound 真 ('true') + 意 ('intention, meaning') — the kind of word used when contrasting surface words with underlying motive. でしょう adds polite probability: not a flat prediction but a confident guess. The whole sentence has a slightly elevated, retrospective register, fitting for a misunderstanding awaiting resolution.