New pictures taken by the New Horizons spacecraft at a different angle as it raced away from Ultima Thule at 31,000mph (50,000 kmh) reveal it is not spherical.
NASA said the larger lobe more closely resembles a giant pancake, and the smaller one a dented walnut.
The images were taken nearly 10 minutes after New Horizons crossed its closest approach point on 1 January.
Scientists also did new analysis of the craft’s approach images to modify their conclusions about its shape.
The mission’s lead scientist, Alan Stern, said: “This really is an incredible image sequence, taken by a spacecraft exploring a small world four billion miles away from Earth.
“Nothing quite like this has ever been captured in imagery.”
The icy world of Ultima Thule is roughly 20 miles long and is the most distant world ever studied by mankind – a billion miles beyond Pluto.
Mr Stern added: “We had an impression of Ultima Thule based on the limited number of images returned in the days around the flyby, but seeing more data has significantly changed our view.”
“It would be closer to reality to say Ultima Thule’s shape is flatter, like a pancake.
“But more importantly, the new images are creating scientific puzzles about how such an object could even be formed. We’ve never seen something like this orbiting the sun.”
NASA says New Horizons’ mission will help scientists understand the origins of our solar system.
Its successful flyby last month sparked scenes of jubilation at the Johns Hopkins Applied Physics Laboratory in Maryland.
Mr Stern said at the time: “Everything we are going to learn about Ultima – from its composition to its geology to how it was originally assembled, whether it has satellites and an atmosphere and those kinds of things – are going to teach us about the original formation conditions of objects in the solar system.”