I think that the strongest source for understanding Thomas Jefferson's racial views is "Notes on the State of Virginia." The document is a thorough exploration of Jefferson's home state, including its flora and fauna, its mountains, and its mineral resources. However, the document is also an exhibition of Jefferson's racism.
Jefferson regarded both indigenous peoples and Black people as inferior to whites. The idea of indigenous and Black peoples as "savage" came out of the Enlightenment, and views about Black people were particularly damning. Both the Scottish empiricist David Hume and Immanuel Kant, who is often deemed the most important philosopher of the modern age, had racist views about black people. For example, Kant, in an encounter with an African, registered surprise when the man said something intelligent. He, like some other Enlightenment thinkers, believed that there was a link between dark skin and poor intellect. This view was not shared by all Enlightenment thinkers, but those who did express racist notions helped to legitimize racism and enslavement.
Like Kant, Jefferson had a physical aversion to Black people. In "Notes on the State of Virginia," he writes about Black people having a peculiar and disagreeable smell. He looks down upon the indigenous man, but allows that he can be civilized and converted to Christianity. Black people, in his view, were incorrigible. All of this is rather ironic, given what we now know about Jefferson's relationship with Sally Hemings, who was at least of one-quarter African descent. However, it's possible that Jefferson distinguished Sally from other Black people, something that might have been easier for him given her lighter complexion.
The view held by Jefferson and some Enlightenment thinkers that Black people were of inferior intelligence and ability made it easy to exclude them from the notion that liberty and equality were natural human rights. Thus, Jefferson wrote in the Declaration of Independence that "all men are created equal" without a hint of irony, for, by this time, Black people were only regarded as three-fifths of a person and naturally subordinate to whites.