Chinese President Xi Jinping will also be in Manila for the Asia-Pacific Economic Cooperation (APEC) summit, an annual event that is meant to forge unity on free trade within the region.
But this year's meeting risks becoming entangled in various US-China power struggles, including over the South China Sea where Chinese island building in disputed waters has caused alarm in the United States and with its Asian allies.
The global menace of terrorism will also be an unwanted talking point after gunmen massacred more than 120 people in a series of coordinated attacks in Paris on Friday.
While China said it wanted the summit to focus only on trade, the French attacks and US attention on the South China Sea showed this was unrealistic, according to Curtis S Chin, a former US ambassador to the Manila-based Asian Development Bank.
"One cannot separate the economic and the non-economic in today's interconnected world," Chin, now an Asia fellow of the Milken Institute, a non-partisan think-tank, told AFP.
China insists it has sovereign rights to nearly all of the sea, even waters approaching the coasts of its Asian neighbours.
The Philippines, Vietnam, Malaysia, Brunei and Taiwan have overlapping claims to some of the waters, which are home to some of the world's most important shipping trade routes.
China's island building in the Spratlys archipelago, which is close to the Philippines, prompted the US military to recently deploy a missile destroyer and B-52 bomber planes to the area.
But US National Security Advisor Susan Rice said the dispute would be a "central issue" during Obama's three-day trip to the Philippines starting on Tuesday, and a subsequent visit to Malaysia for another regional summit.
Rice also emphasised Obama would raise the issues of "maritime security" and "freedom of navigation", terms commonly used when referring to the dispute.
The Philippines, which has hauled China before a United Nations tribunal over the row, initially promised to respect that demand.
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