The spacecraft is scheduled to fly past the Kuiper Belt object (KBO) 2014 MU69 on January 1, 2019.
New data gathered on the object suggest it could well be two bodies that are close together or even touching.
"This new finding is simply spectacular. The shape of MU69 is truly provocative, and could mean another first for New Horizons going to a binary object in the Kuiper Belt," said Alan Stern, mission principal investigator from the Southwest Research Institute (SwRI) in Boulder, Colorado.
The Kuiper Belt is a disc-shaped region of icy bodies - including dwarf planets such as Pluto - and comets beyond the orbit of Neptune.
NASA said the ancient KBO, which is more than 6.5 billion kilometeres from Earth, passed in front of a star on July 17, 2017.
A handful of telescopes deployed by the New Horizons team in a remote part of Patagonia, Argentina were in the right place at the right time to catch its fleeting shadow -- an event known as an occultation.
They were able to capture important data to help mission flyby planners better determine the spacecraft trajectory and understand the size, shape, orbit and environment around MU69.
Based on these new occultation observations, scientists speculate that the Kuiper Belt object could be a single body with a large chunk taken out of it, or two bodies.
The size of MU69 appears to be no more than 30 kilometres long, or, if a binary, each about 15-20 kilometeres in diameter, according to the scientists.
"These exciting and puzzling results have already been key for our mission planning, but also add to the mysteries surrounding this target leading into the New Horizons encounter with MU69, now less than 17 months away," Marc Buie, the New Horizons co-investigator who led the observation campaign, said.
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