BEIJING — The Philippines has won an important ruling in its case against China over disputed parts of the South China Sea, with an arbitration court in the Netherlands saying it has jurisdiction in the case and will hold hearings.

The Permanent Court of Arbitration in The Hague issued the ruling on Thursday, in proceedings that China has boycotted since the Philippines, an ally of the United States, filed suit at the court in 2013.

The ruling was a blow to China, which had hoped the court would reject jurisdiction, allowing Beijing to continue making a case that its claims in the South China Sea are based on history rather than legal precedent.

The Philippines welcomed the decision on Friday and said it was prepared to argue the merits of its case before the tribunal. “Our people can be assured that those representing our country have been continuously preparing for this,” said Abigail Valte, a spokeswoman for the Philippine president, Benigno S. Aquino III.