So far as we can tell, Jefferson was clearly aware of the fact that slavery was morally wrong.  It appears that he simply could not bring himself to take the financial hit that would have resulted from freeing his own slaves.

Jefferson was willing to do things that were anti-slavery.  For example, he was a supporter of the Northwest Ordinance, which banned slavery in the territories of what was then the northwest.  He also advocated gradual emancipation of slaves.

At the same time, Jefferson worked to rationalize the fact that he owned slaves.  He clearly believed that blacks were inferior to whites.  He therefore would cast himself as a parent figure with respect to his slaves.  That is, he could at least tell himself that slavery was acceptable in his case because his slaves were inferior to him and needed his guidance.

We do not know for sure how clearly Jefferson saw the hypocrisy of his views on slavery given the fact that he owned slaves.  However, it seems likely that he was aware of that hypocrisy to some degree and felt the need to rationalize it away.