Ms Nandy, who has represented Wigan since 2010, supported the bill and had argued for others to do the same.
In the Commons, she voiced her opinion that the deal must be allowed to "proceed to committee stage" to allow it to be scrutinised further, stating a will to improve it and insisted her support was not guaranteed at a third reading.
Labour leader Jeremy Corbyn told her he understood the concerns of MPs such as her, from Leave backing communities, though still urged her to vote against it.
However, she has been blasted over email after following through on her stance, branded "total scum" and "despicable".
She shared too screengrabs of messages on her Twitter, with the caption: "Morning!"
One message said: "You should have your fat a*** kicked out of the party. I don't know how anyone could walk past you without holding their nose. I hope you rot in hell."
While the second said: "Your utter, selfish, ignorance has just LOST Labour any chance of winning an election."
It ended: "I will never vote Labour again."
It comes days after she shared a similar abusive message sent to her which called her "far more a fascist than a socialist".
Ms Nandy, despite backing the bill at second reading, voted against the Government's fast-track motion for the Brexit legislation.
The Government won the first vote but lost the latter.
Writing on Twitter late last night, she said: "In my view you betray the people you represent when you believe that your own moral purity and principles come before trying to improve things for others, however hard. I could stand on the sidelines and wave a flag, or make some decisions. I choose to try."
The abuse to Ms Nandy comes after Labour MP Harriet Harman said politicians were scared to use public transport due to the growing threat of violence.
She told Sky: “There is a growing minority who make threats and actually carry out violence.
"What is really sad to see is MPs are less likely to go out and about on the bus and train on their own as we always used to do, less likely to have advice surgeries where people can just drop in without an appointment.
"You can see MPs offices being daubed with threatening graffiti. That’s not the sort of country we are. It’s only a minority but they are dangerous."