My understanding is that Jefferson was very much opposed to slavery. He believed that abolition had to be a gradual process, first with the abolition of the slave trade, then encouraging the growth of crops that did not require cultivation by slaves (e.g.: wheat and wine grapes rather than tobacco), until slave owners would willingly give up their slaves.
His want of gradual, as opposed to immediate, abolition was because he was afraid that such an action would be perceived as contrary to States' right, etc. and therefore risk civil war. However, this was not a problem when it involved only him and his slaves, so why not free them, while working towards gradual abolition?
u/sowser's post identifies Jefferson's racist thinking . But a key reason for his not freeing his slaves must also have been his great debts. For one thing, his slaves were property, and mortgaged: yes, mortgaged to some friendly lenders, so his other creditors couldn't simply show up and seize them. But in order to actually free them he would have had to buy back their mortgages, and that would have been very expensive. When he died, there was no money for that and they were sold. For another, he leased them out, had them work on his farms...his slaves gave him an income to help manage those debts. They were how he was able to live the life of a Virginia aristocrat with plenty of free time for writing and inventing and a wine cellar for entertaining.
That Jefferson would write eloquently against slavery but profit by it is in character with the man. Jefferson could sometimes exempt himself from the principles he envisaged for the rest of the world. He surprised many of his fellow revolutionaries by retreating to his farm after writing the Declaration, instead of joining in the fight ( they had to beg him to come and help). And he had a harpsichord smuggled into Virginia in the middle of the Revolution when, in theory, there was a ban on such foreign imports because he said he just had to have one. He's been called the American Sphinx for good reason: the difference between what he said and what he did can make it hard to understand precisely what he was thinking.
Not to discourage further discussion since, for historians, nothing is ever the final say, but u/sowser wrote a bit [here] (https://www.reddit.com/r/AskHistorians/comments/4qxzdx/how_did_thomas_jefferson_reconcile_all_men_are/d4wsl8a?utm_source=reddit-android) where he references an essay he wrote that has helped a few people unpack Jefferson's seemingly contradictory statements.