CHOEUNG EK, Cambodia — With opening statements about to begin in the most important phase of the Khmer Rouge trials, survivors of the regime’s violence kneeled before a huge pyramid of skulls at a killing field here on Sunday as monks chanted a prayer for the souls of the dead.

Chickens pecked in the damp grass above the pits where nearly 9,000 people were bludgeoned to death and where teeth and bits of bone still work their way to the surface during monsoon floods. Signs warn tourists, “Please don’t walk through the mass grave.”

In the trial that got under way on Monday, three senior members of the Khmer Rouge leadership faced charges of genocide, crimes against humanity, war crimes and other charges....