The 52-year-old star and the rocker, 62, apparently could not sustain the long-distance relationship, reported People magazine.
"It was the distance. She lives in New York and he resides in Indiana. It was the long distance that ultimately was the cause," a source said.
The pair, who was last spotted together in May, started dating shortly after Mellencamp's split from wife Elaine in 2010, after 18 years of marriage.
They kept a low profile during the past three years, stepping out together for the occasional industry event and being spotted now and again on the streets of New York.
"I can't see the suffering. I can't see the trash on the streets. I'm not leaving Indiana. I'm going to die here," he had said in an interview in last December.
Representative for the pair have not commented yet.