Around 600 delegates will assemble in the northern city of Hanover for the two-day event, with pro-refugee protests and police on hand.
The AfD won nearly 13 percent in September's general election, taking almost 100 seats in parliament on an anti- immigration and anti-Muslim platform.
Its main rallying cry was "Merkel must go" following her decision to let in more than one million asylum seekers since 2015.
The AfD has relished the chancellor's woes since the poll left her without a clear ruling majority and now tied up in protracted coalition talks.
The main order of business will be the election of new leadership after the dramatic departure in September of its best-known figure, Frauke Petry.
While co-leader Joerg Meuthen is standing for re- election, he is facing a challenge from the party's Berlin chief, Georg Pazderski.
AfD parliamentary group president Alexander Gauland urged the party to continue having two leaders, saying it helped bridge internal divisions.
"It is crucial to me that the top of the AfD reflects east and west as well as more conservative and economically liberal positions," he told AFP.
Although the sudden exit reinforced an image of infighting, Petry failed to lure more than just one MP to join her in defecting.
"She apparently hoped to take more people with her and then it didn't happen," Gauland said.
"The parliamentary group is working together harmoniously," he insisted.
It is also possible that Bjoern Hoecke, who has triggered outrage with calls for Germany to back away from its atonement for World War II crimes, will stand in Hanover for the party's 13-member board.
"Hoecke and his supporters are in the radical nationalist wing of the party," Berlin's Tagesspiegel newspaper said.
"If they are strongly represented on the new board, it would be seen as a rightward lurch for the party... possibly prompting many relatively moderate members to leave."
The congress comes at a time of great uncertainty for Germany, with suspense building as to how the current deadlock in Europe's top economy can end.
Merkel held four weeks of talks with the pro-business Free Democrats and the ecologist Greens to form an unprecedented alliance spanning the political spectrum but the negotiations collapsed in acrimony earlier this month.
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