Briton Murray, seeded second, has won seven of eight previous matches against Japan's Nishikori, the most recent being at last month's Olympics.
The pair are scheduled second on Arthur Ashe Stadium at around 19:00 BST.
"I've played well against him in the past but he likes these conditions," said the 29-year-old world number two.
"I played a really good match against him when we played a few weeks ago. I'm aware I'll need to do that again if I want to beat him, because he's one of the best players in the world."
The winner will face Argentina's Juan Martin Del Potro or Swiss third seed Stan Wawrinka, who meet in the night session at about 02:00 on Thursday.
They follow the women's quarter-final between world number one Serena Williams and fifth seed Simona Halep at 00:00, with Karolina Pliskova and Ana Konjuh opening Wednesday's play at 17:00.
Jamie Murray and Brazil's Bruno Soares take on Australian Chris Guccione and Brazilian Andre Sa in the doubles quarter-finals at 16:00.
Andy Murray will hope to extend an impressive record against sixth seed Kei Nishikori when the pair meet in the US Open quarter-finals on Wednesday.