It means the people are the boss. Not a parliament, not a president, not a court, but the people themselves are the ultimate source of all government power.
Popular sovereignty is the principle that ultimate political authority rests with the people. Every legitimate power of government is, in the end, on loan from them. The word sovereignty once meant the supreme power of a king; this idea relocates it to the citizenry.
The Constitution announces it in its first three words. We the People, written large, declares who is doing the establishing. The government does not create the people; the people create the government, and say so at the very top of the document.
It reframes everything beneath it. Officials are not masters but representatives, exercising borrowed power. The Constitution itself can be amended by the people's processes, because the people who made it retain the authority to change it.
The phrase later took on a second, troubled meaning in the 1850s, when popular sovereignty was used to argue that settlers in a territory should vote on whether to allow slavery, a use that led to bloodshed in Kansas. The core idea, though, remains the people as the source of power.