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.
China’s Foreign Ministry said the country would not accept any ruling from the court, a standard statement from the ministry on the case. It accused the Philippines of “a political provocation under the cloak of law.”
The case is being closely watched by the United States and other Asian nations that are claimants in the South China Sea, where China asserts sovereignty over islands and reefs within about 90 percent of the strategic waterway.
The Philippines — represented by an American lawyer, Paul Reichler, of the Washington law firm Foley Hoag — contends that it has the right to exploit oil and gas in waters in a 200-nautical-mile exclusive economic zone extending from territory that it claims in the South China Sea.
The Hague court rejected Beijing’s claims that the disputes in the sea are about its territorial sovereignty, which China says is based on historical rights and is indisputable.
Mr. Reichler made his arguments in July before the court, which was established in 1899 to encourage the peaceful resolution of international disputes. There had been speculation about whether the court would accept the case, given China’s absence from the proceedings.
The court ruled on Thursday that it had the authority to hear the Philippines’s submissions, which are based on the United Nations Convention on the Law of the Sea, a set of laws that the United States has not signed but uses as the basis of its policies in the heated contest with China over the South China Sea.
This week, an American destroyer, the Lassen, sailed within 12 nautical miles of Subi Reef, in the Spratly archipelago near the Philippines, which China has built into an artificial island. A Chinese military airstrip is under construction on the island.
The American naval operation was devised to show that the new island does not have a 12-mile territorial zone. The Law of the Sea says that bits of rock or reef that are elevated only at low tide are not entitled to such a zone.
In part of its case, the Philippines argues that China has prevented Philippine vessels from exploiting the waters adjacent to Scarborough Shoal and Johnson Reef, two small outcrops favored by fishermen.
In 2012, China put a barrier across the entrance to Scarborough Shoal that prevented Philippine fishing boats from entering its waters. A deal brokered by the United States that called for both countries to withdraw from the shoal soon fell apart.
Jay Batongbacal, the director of the Institute for Maritime Affairs and Law of the Sea at the University of the Philippines, said the ruling would be useful in diplomatic negotiations with other countries that oppose China’s actions in the South China Sea. “The ruling could act to embolden and bring unity to the other claimants,” he said.
Zhu Feng, the executive director of the China Center for Collaborative Studies of the South China Sea at Nanjing University, said the ruling was not a defeat for China, adding, “The international jurisdiction will always move in its own way.” But he said he supported the idea of China becoming more involved in the court proceedings.
“I hope Beijing could become more active in participating in all forums and respond to the international ruling at the tribunal,” he said.
Floyd Whaley contributed reporting from Manila. Yufan Huang contributed research.
A version of this article appears in print on October 31, 2015, on page A8 of the New York edition with the headline: Hague Court Will Hear Case on Isles in China Sea.