The 27-year-old swimmer had equalled Larisa Latynina's record earlier this evening with silver in the 200m Butterfly.
But the USA swimmer has now moved beyond the Russian, whose record had stood since 1964, to stand alone at the pinnacle with three more events to come.
Phelps was just touched out for gold in the 200m Butterfly by Chad le Clos of South Africa, with Takeshi Matsuda claiming the bronze for Japan.
Earlier, teenager Ye Shiwen added the 200m Individual Medley title to the gold she won in the 400m IM.
The 16-year-old came from slightly down at third at the final turn to produce a storming freestyle leg to secure victory.
Meanwhile, USA's Allison Schmitt won in Olympic record time in the 200m Freestyle final.
Schmitt, who last month swam the event faster than anyone in textiles in history, led from start to finish and touched in a dominant 1:53.61.
France's Camille Muffat was second as the pair reversed their placings in the 400m Freestyle on Sunday.