Heavy snow and flooding is expected to hit New York, Philadelphia and other cities from Monday until Tuesday evening.
The carrier said only the section between Dubai and Athens would operate.
Emirates said affected passengers are being rebooked on alternate flights to their destinations.
“We are closely monitoring the situation. We apologise for any inconvenience, the safety of our crew and passengers is of the utmost importance,” it said.
Abu Dhabi rival Etihad also cancelled its Tuesday EY103 flight from Abu Dhabi to New York and the return journey.
It said EY101 to New York would be upgraded to an Airbus A380 to accommodate passengers affected by the cancellation but warned this too could be delayed.
However, services to Washington and Chicago are operating as scheduled, according to the carrier.
The cancellations came as the UAE Embassy to the US warned nationals on the East coast to stay tuned to local weather alerts.