The motion was approved by 479 votes to 37, with 107 abstentions.
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 following the July 15 failed coup attempt.
Thursday's motion comes as Ankara has been fighting the Gülenist Terror Group (FETÖ) following Turkey's defeated coup attempt on July 15. Tens of thousands of state employees have been dismissed over suspected links to FETÖ.President Recep Tayyip Erdoğan has already dismissed the vote as having "no value" as it is non-binding, and as most European Union member states so far want to keep the Turkey talks on track.
The Ministry for EU Affairs released a statement regarding the vote on Turkey-EU relations, saying that the European Council has the final decision-making power to temporarily suspend membership negotiations.
"Even if a decision suggesting the suspension of negotiations with Turkey is made after voting in the European Parliament, such a decision will not be legally binding" the statement added.
Earlier in the week, EU foreign policy chief Federica Mogherini warned that halting Turkey's accession process would be a "lose-lose" move.
President Erdoğan warned the EU last week to make a decision by year's end on Turkey's membership or he would call a referendum on the matter.
Last Friday, European Parliament President Martin Schulz said he hopes Turkey will not give up on negotiations for the country to be part of the European Union, and that such a move would not be a win for Europe.
Relations between Turkey and Europe have been stalled by many issues, including the failure of the EU to grant visa liberalization for Turkish citizens as promised and EU's indifference to the coup attempt and terrorist organizations attacking Turkey.
The EU and Turkey signed a refugee deal on March 18, which aimed to discourage irregular migration through the Aegean Sea by taking stricter measures against human traffickers and improving the conditions of nearly 3 million Syrian refugees in Turkey.
Although Turkey has fulfilled most of the criteria, differences between Brussels and Ankara on anti-terror legislation have forestalled the visa-liberalization deal.
Ankara criticized the European Union's stance on the PKK terror group and FETÖ, saying EU states are turning a blind eye to the terror attacks against the Turkish state and its people as well as the activities of the group within the borders of the EU.
Turkey began its EU accession talks in 2005. In 1963, Turkey and the European Economic Community (the EU's former name) signed an association agreement.