The Philippines and China have exchanged accusations of intentionally ramming coast guard vessels in the disputed waterway in recent months, including a violent clash in June in which a Filipino sailor lost a finger.
The incidents have overshadowed efforts by both nations to rebuild trust and better manage confrontations, including setting up new lines of communication to improve handling maritime disputes.
"China-Philippines relations stand at a crossroads, facing a choice of which way to go," the commentary said. "Dialogue and consultation is the right path, as there is no way out of the conflict through confrontation."
Manila "should seriously consider the future of China-Philippines relations and work with China to push bilateral relations back on track," it added.
The commentary was published under the pen name "Zhong Sheng", meaning "Voice of China", which is often used to give the paper's view on foreign policy issues.
Beijing claims almost the entire South China Sea, including parts claimed by the Philippines, Brunei, Malaysia, Taiwan and Vietnam. Portions of the waterway, where $3 trillion worth of trade passes annually, are believed to be rich in oil and natural gas deposits, as well as fish stocks.
The Permanent Court of Arbitration in 2016 found China's sweeping claims had no legal basis, a ruling Beijing rejects.
In June, the United States reaffirmed its commitment to the Philippines' security, after Manila accused China of a "deliberate action" to stop the resupply of Philippine troops stationed at the disputed Second Thomas Shoal.
In Monday's commentary, China blamed the Philippines for "the so-called 'humanitarian' problem" that Filipino sailors aboard what China considers "an illegally stranded ship" at nearby Sabina Shoal had no access to supplies, adding "the people aboard are absolutely allowed to leave."