A primary source is the original document about a topic - that's why it is called a primary, or first, source. In your history class, if you were learning about the Revolutionary War, for example, by reading diaries that had been written by people who were alive at that time and were involved in activities connected with the events, those would be primary sources. If you were learning about the Revolutionary War by reading about it in a textbook, that would be using a secondary source.
In the case of your question, the primary source of the Three-Fifths Compromise is the document in which that compromise is found, the United States Constitution. Article I Section 2 spells out the arrangement that allowed slave states to claim "three fifths of all other Persons" as part of their state's population for purposes of representation in the House of Representatives.