By 479 votes to 37, with 107 abstentions, lawmakers backed a motion calling on "the Commission and on the Member States to initiate a temporary freeze of the ongoing accession negotiations with Turkey".
MEPs agreed on nine clauses which include the 'freeze' expression, arguing Turkey is violating seven of 72 criteria crucial for the continuation of membership talks.
The text said Turkey used “non-proportional security measures” during the country’s state of emergency, extended for another 90 days in October.
Thursday's motion comes as Ankara has been fighting the Fetullah Terrorist Organization (FETO) following Turkey’s defeated coup attempt on July 15. Tens of thousands of state employees have been dismissed over suspected links to FETO.
The text also claimed "serious concerns have been raised over the conditions of those detained and arrested following the attempted coup and over the severe restrictions on freedom of expression and on the press and media in Turkey”.
Turkey formally applied to become an EU member in 1987; accession talks began in 2005.
President Recep Tayyip Erdogan said on Wednesday the vote would have "no value" in Turkish eyes.
EU foreign policy chief Federica Mogherini warned on Tuesday that halting Turkey's accession process would be a “lose-lose” scenario.
Carl Bildt, former Swedish prime minister, said in a Twitter post ahead of the vote: “Obvious that many in European Parliament take a populist short-term rather than strategic long-term approach to relations which Turkey,”
“It would be a strategic stupidity of the first order for the EU to unilaterally abandon its relationship with Turkey.”